Deep structured output learning shows great promise in tasks like semantic image segmentation. We proffer a new, efficient deep structured model learning scheme, in which we show how deep Convolutional Neural Networks (CNNs) can be used to estimate the messages in message passing inference for structured prediction with Conditional Random Fields (CRFs). With such CNN message estimators, we obviate the need to learn or evaluate potential functions for message calculation. This confers significant efficiency for learning, since otherwise when performing structured learning for a CRF with CNN potentials it is necessary to undertake expensive inference for every stochastic gradient iteration. The network output dimension for message estimation is the same as the number of classes, in contrast to the network output for general CNN potential functions in CRFs, which is exponential in the order of the potentials. Hence CNN message learning has fewer network parameters and is more scalable for cases that a large number of classes are involved. We apply our method to semantic image segmentation on the PASCAL VOC 2012 dataset. We achieve an intersection-over-union score of 73.4 on its test set, which is the best reported result for methods using the VOC training images alone. This impressive performance demonstrates the effectiveness and usefulness of our CNN message learning method.

This is the author's version which is being continuously updated and not synchronised with the journal version. The final printed version will appear in Briefings in Bioinformatics Abstract Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info. 1 Introduction The nucleosome is the basic unit of chromatin compaction, composed of the histone octamer and 146-147 base pairs (bp) of DNA wrapped around it. Nucleosomes can form at any genomic locations, but some DNA sequences have higher affinity to the histone octamer, mostly due to the differential bending properties of the DNA double helix. In addition, nucleosome positioning is cell type-specific, in a sense that the cells of the same organism sharing the same genome can have different nucleosome locations depending on the cell type and state. Interested readers are directed to a number of recent publications reviewing the biological, physical and bioinformatics aspects of these phenomena, which will be outside of the scope of the current work [1-32]. Here we will omit fundamental scientific questions, and will focus on a very practical aspect of the field: which experimental nucleosome positioning datasets already exist, how to generate your own data, and how to compare these with other experimental datasets and bioinformatically predicted nucleosome positions in a given genome? 1. Available experimental datasets Recent high-throughput genome-wide data with respect to nucleosome positioning come from a number of related techniques, which have in common an idea to cut DNA between nucleosomes and map protected DNA regions. The most frequently used method is MNase-seq (chromatin digestion by micrococcal nuclease followed by deep sequencing) [11, 33-35].

This text investigates relations between two well-known family of algorithms, matrix factorisations and recursive linear filters, by describing a probabilistic model in which approximate inference corresponds to a matrix factorisation algorithm. Using the probabilistic model, we derive a matrix factorisation algorithm as a recursive linear filter. More precisely, we derive a matrix-variate recursive linear filter in order to perform efficient inference in high dimensions. We also show that it is possible to interpret our algorithm as a nontrivial stochastic gradient algorithm. Demonstrations and comparisons on an image restoration task are given.

While some particles can be identified by their type, such as electrons [3, 4] and muons [5, 6], most of the detected particles are light hadrons produced in collimated sprays called jets. Jets are the consequence of high energy quarks or gluons fragmenting into colorless hadrons. Experimentally, jets are defined by clustering schemes which group together measured calorimeter energy deposits or reconstructed charged particle tracks. A jet algorithm is a clustering scheme that connects the measured objects with theoretical quantities that can be calculated and simulated. At a hadron collider, the natural coordinates for describing particles arep T, y, and φ, where p T is the magnitude of the momentum transverse to the proton beam,y is the rapidity, andφ is the azimuthal angle. Particles or calorimeter energy deposits are clustered using jet algorithms based on distance metrics on their coordinates in (p T, ρ) (p T,y,φ) . In order for a jet algorithm to be useful to experimentalists and theorists, the collection of jets should be IRC safe in the following sense: 1. Infrared safe (IR): if a particlei is added with p T 0, the jets are unaffected.

Crowdsourcing utilizes the wisdom of crowds for collective classification via information (e.g., labels of an item) provided by labelers. Current crowdsourcing algorithms are mainly unsupervised methods that are unaware of the quality of crowdsourced data. In this paper, we propose a supervised collective classification algorithm that aims to identify reliable labelers from the training data (e.g., items with known labels). The reliability (i.e., weighting factor) of each labeler is determined via a saddle point algorithm. The results on several crowdsourced data show that supervised methods can achieve better classification accuracy than unsupervised methods, and our proposed method outperforms other algorithms.

The growing need for labeled training data has made crowdsourcing an important part of machine learning. The quality of crowdsourced labels is, however, adversely affected by three factors: (1) the workers are not experts; (2) the incentives of the workers are not aligned with those of the requesters; and (3) the interface does not allow workers to convey their knowledge accurately, by forcing them to make a single choice among a set of options. In this paper, we address these issues by introducing approval voting to utilize the expertise of workers who have partial knowledge of the true answer, and coupling it with a ("strictly proper") incentive-compatible compensation mechanism. We show rigorous theoretical guarantees of optimality of our mechanism together with a simple axiomatic characterization. We also conduct preliminary empirical studies on Amazon Mechanical Turk which validate our approach.

We theoretically and experimentally investigate tensor-based regression and classification. Our focus is regularization with various tensor norms, including the overlapped trace norm, the latent trace norm, and the scaled latent trace norm. We first give dual optimization methods using the alternating direction method of multipliers, which is computationally efficient when the number of training samples is moderate. We then theoretically derive an excess risk bound for each tensor norm and clarify their behavior. Finally, we perform extensive experiments using simulated and real data and demonstrate the superiority of tensor-based learning methods over vector- and matrix-based learning methods.

In this paper, we study different discrete data clustering methods, which use the Model-Based Clustering (MBC) framework with the Multinomial distribution. Our study comprises several relevant issues, such as initialization, model estimation and model selection. Additionally, we propose a novel MBC method by efficiently combining the partitional and hierarchical clustering techniques. We conduct experiments on both synthetic and real data and evaluate the methods using accuracy, stability and computation time. Our study identifies appropriate strategies to be used for discrete data analysis with the MBC methods. Moreover, our proposed method is very competitive w.r.t.

Nonnegative matrix factorization (NMF) has an established reputation as a useful data analysis technique in numerous applications. However, its usage in practical situations is undergoing challenges in recent years. The fundamental factor to this is the increasingly growing size of the datasets available and needed in the information sciences. To address this, in this work we propose to use structured random compression, that is, random projections that exploit the data structure, for two NMF variants: classical and separable. In separable NMF (SNMF) the left factors are a subset of the columns of the input matrix. We present suitable formulations for each problem, dealing with different representative algorithms within each one. We show that the resulting compressed techniques are faster than their uncompressed variants, vastly reduce memory demands, and do not encompass any significant deterioration in performance. The proposed structured random projections for SNMF allow to deal with arbitrarily shaped large matrices, beyond the standard limit of tall-and-skinny matrices, granting access to very efficient computations in this general setting. We accompany the algorithmic presentation with theoretical foundations and numerous and diverse examples, showing the suitability of the proposed approaches.

Department of Computing Imperial College London 180 Queen's Gate London SW7 2RH United Kingdom April 2015 Abstract This paper critically assesses the anti-functionalist stance on consciousness adopted by certain advocates of integrated information theory (IIT), a corollary of which is that human-level artificial intelligence implemented on conventional computing hardware is necessarily not conscious. The critique draws on variations of a well-known gradual neuronal replacement thought experiment, as well as bringing out tensions in IIT's treatment of self-knowledge. The aim, though, is neither to reject IIT outright nor to champion functionalism in particular. Rather, it is suggested that both ideas have something to offer a scientific understanding of consciousness, as long as they are not dressed up as solutions to illusory metaphysical problems. As for human-level AI, we must await its development before we can decide whether or not to ascribe consciousness to it.