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Framework for Multi-task Multiple Kernel Learning and Applications in Genome Analysis

arXiv.org Machine Learning

We present a general regularization-based framework for Multi-task learning (MTL), in which the similarity between tasks can be learned or refined using $\ell_p$-norm Multiple Kernel learning (MKL). Based on this very general formulation (including a general loss function), we derive the corresponding dual formulation using Fenchel duality applied to Hermitian matrices. We show that numerous established MTL methods can be derived as special cases from both, the primal and dual of our formulation. Furthermore, we derive a modern dual-coordinate descend optimization strategy for the hinge-loss variant of our formulation and provide convergence bounds for our algorithm. As a special case, we implement in C++ a fast LibLinear-style solver for $\ell_p$-norm MKL. In the experimental section, we analyze various aspects of our algorithm such as predictive performance and ability to reconstruct task relationships on biologically inspired synthetic data, where we have full control over the underlying ground truth. We also experiment on a new dataset from the domain of computational biology that we collected for the purpose of this paper. It concerns the prediction of transcription start sites (TSS) over nine organisms, which is a crucial task in gene finding. Our solvers including all discussed special cases are made available as open-source software as part of the SHOGUN machine learning toolbox (available at \url{http://shogun.ml}).


Divide-and-Conquer with Sequential Monte Carlo

arXiv.org Machine Learning

We propose a novel class of Sequential Monte Carlo (SMC) algorithms, appropriate for inference in probabilistic graphical models. This class of algorithms adopts a divide-and-conquer approach based upon an auxiliary tree-structured decomposition of the model of interest, turning the overall inferential task into a collection of recursively solved sub-problems. The proposed method is applicable to a broad class of probabilistic graphical models, including models with loops. Unlike a standard SMC sampler, the proposed Divide-and-Conquer SMC employs multiple independent populations of weighted particles, which are resampled, merged, and propagated as the method progresses. We illustrate empirically that this approach can outperform standard methods in terms of the accuracy of the posterior expectation and marginal likelihood approximations. Divide-and-Conquer SMC also opens up novel parallel implementation options and the possibility of concentrating the computational effort on the most challenging sub-problems. We demonstrate its performance on a Markov random field and on a hierarchical logistic regression problem.


Probabilistic Inference Techniques for Scalable Multiagent Decision Making

Journal of Artificial Intelligence Research

Decentralized POMDPs provide an expressive framework for multiagent sequential decision making. However, the complexity of these models---NEXP-Complete even for two agents---has limited their scalability. We present a promising new class of approximation algorithms by developing novel connections between multiagent planning and machine learning. We show how the multiagent planning problem can be reformulated as inference in a mixture of dynamic Bayesian networks (DBNs). This planning-as-inference approach paves the way for the application of efficient inference techniques in DBNs to multiagent decision making. To further improve scalability, we identify certain conditions that are sufficient to extend the approach to multiagent systems with dozens of agents. Specifically, we show that the necessary inference within the expectation-maximization framework can be decomposed into processes that often involve a small subset of agents, thereby facilitating scalability. We further show that a number of existing multiagent planning models satisfy these conditions. Experiments on large planning benchmarks confirm the benefits of our approach in terms of runtime and scalability with respect to existing techniques.


Compressed Sensing of Multi-Channel EEG Signals: The Simultaneous Cosparsity and Low Rank Optimization

arXiv.org Machine Learning

Goal: This paper deals with the problems that some EEG signals have no good sparse representation and single channel processing is not computationally efficient in compressed sensing of multi-channel EEG signals. Methods: An optimization model with L0 norm and Schatten-0 norm is proposed to enforce cosparsity and low rank structures in the reconstructed multi-channel EEG signals. Both convex relaxation and global consensus optimization with alternating direction method of multipliers are used to compute the optimization model. Results: The performance of multi-channel EEG signal reconstruction is improved in term of both accuracy and computational complexity. Conclusion: The proposed method is a better candidate than previous sparse signal recovery methods for compressed sensing of EEG signals. Significance: The proposed method enables successful compressed sensing of EEG signals even when the signals have no good sparse representation. Using compressed sensing would much reduce the power consumption of wireless EEG system.


Using Machine Translation to Provide Target-Language Edit Hints in Computer Aided Translation Based on Translation Memories

Journal of Artificial Intelligence Research

This paper explores the use of general-purpose machine translation (MT) in assisting the users of computer-aided translation (CAT) systems based on translation memory (TM) to identify the target words in the translation proposals that need to be changed (either replaced or removed) or kept unedited, a task we term as "word-keeping recommendation". MT is used as a black box to align source and target sub-segments on the fly in the translation units (TUs) suggested to the user. Source-language (SL) and target-language (TL) segments in the matching TUs are segmented into overlapping sub-segments of variable length and machine-translated into the TL and the SL, respectively. The bilingual sub-segments obtained and the matching between the SL segment in the TU and the segment to be translated are employed to build the features that are then used by a binary classifier to determine the target words to be changed and those to be kept unedited. In this approach, MT results are never presented to the translator. Two approaches are presented in this work: one using a word-keeping recommendation system which can be trained on the TM used with the CAT system, and a more basic approach which does not require any training. Experiments are conducted by simulating the translation of texts in several language pairs with corpora belonging to different domains and using three different MT systems. We compare the performance obtained to that of previous works that have used statistical word alignment for word-keeping recommendation, and show that the MT-based approaches presented in this paper are more accurate in most scenarios. In particular, our results confirm that the MT-based approaches are better than the alignment-based approach when using models trained on out-of-domain TMs. Additional experiments were performed to check how dependent the MT-based recommender is on the language pair and MT system used for training. These experiments confirm a high degree of reusability of the recommendation models across various MT systems, but a low level of reusability across language pairs.


Clause Elimination for SAT and QSAT

Journal of Artificial Intelligence Research

The famous archetypical NP-complete problem of Boolean satisfiability (SAT) and its PSPACE-complete generalization of quantified Boolean satisfiability (QSAT) have become central declarative programming paradigms through which real-world instances of various computationally hard problems can be efficiently solved. This success has been achieved through several breakthroughs in practical implementations of decision procedures for SAT and QSAT, that is, in SAT and QSAT solvers. Here, simplification techniques for conjunctive normal form (CNF) for SAT and for prenex conjunctive normal form (PCNF) for QSAT---the standard input formats of SAT and QSAT solvers---have recently proven very effective in increasing solver efficiency when applied before (i.e., in preprocessing) or during (i.e., in inprocessing) satisfiability search. In this article, we develop and analyze clause elimination procedures for pre- and inprocessing. Clause elimination procedures form a family of (P)CNF formula simplification techniques which remove clauses that have specific (in practice polynomial-time) redundancy properties while maintaining the satisfiability status of the formulas. Extending known procedures such as tautology, subsumption, and blocked clause elimination, we introduce novel elimination procedures based on asymmetric variants of these techniques, and also develop a novel family of so-called covered clause elimination procedures, as well as natural liftings of the CNF-level procedures to PCNF. We analyze the considered clause elimination procedures from various perspectives. Furthermore, for the variants not preserving logical equivalence under clause elimination, we show how to reconstruct solutions to original CNFs from satisfying assignments to simplified CNFs, which is important for practical applications for the procedures. Complementing the more theoretical analysis, we present results on an empirical evaluation on the practical importance of the clause elimination procedures in terms of the effect on solver runtimes on standard real-world application benchmarks. It turns out that the importance of applying the clause elimination procedures developed in this work is empirically emphasized in the context of state-of-the-art QSAT solving.


An Empirical Study of Stochastic Variational Algorithms for the Beta Bernoulli Process

arXiv.org Machine Learning

Stochastic variational inference (SVI) is emerging as the most promising candidate for scaling inference in Bayesian probabilistic models to large datasets. However, the performance of these methods has been assessed primarily in the context of Bayesian topic models, particularly latent Dirichlet allocation (LDA). Deriving several new algorithms, and using synthetic, image and genomic datasets, we investigate whether the understanding gleaned from LDA applies in the setting of sparse latent factor models, specifically beta process factor analysis (BPFA). We demonstrate that the big picture is consistent: using Gibbs sampling within SVI to maintain certain posterior dependencies is extremely effective. However, we find that different posterior dependencies are important in BPFA relative to LDA. Particularly, approximations able to model intra-local variable dependence perform best.


Finding Linear Structure in Large Datasets with Scalable Canonical Correlation Analysis

arXiv.org Machine Learning

Canonical Correlation Analysis (CCA) is a widely used spectral technique for finding correlation structures in multi-view datasets. In this paper, we tackle the problem of large scale CCA, where classical algorithms, usually requiring computing the product of two huge matrices and huge matrix decomposition, are computationally and storage expensive. We recast CCA from a novel perspective and propose a scalable and memory efficient Augmented Approximate Gradient (AppGrad) scheme for finding top $k$ dimensional canonical subspace which only involves large matrix multiplying a thin matrix of width $k$ and small matrix decomposition of dimension $k\times k$. Further, AppGrad achieves optimal storage complexity $O(k(p_1+p_2))$, compared with classical algorithms which usually require $O(p_1^2+p_2^2)$ space to store two dense whitening matrices. The proposed scheme naturally generalizes to stochastic optimization regime, especially efficient for huge datasets where batch algorithms are prohibitive. The online property of stochastic AppGrad is also well suited to the streaming scenario, where data comes sequentially. To the best of our knowledge, it is the first stochastic algorithm for CCA. Experiments on four real data sets are provided to show the effectiveness of the proposed methods.


Joint community and anomaly tracking in dynamic networks

arXiv.org Machine Learning

Most real-world networks exhibit community structure, a phenomenon characterized by existence of node clusters whose intra-edge connectivity is stronger than edge connectivities between nodes belonging to different clusters. In addition to facilitating a better understanding of network behavior, community detection finds many practical applications in diverse settings. Communities in online social networks are indicative of shared functional roles, or affiliation to a common socio-economic status, the knowledge of which is vital for targeted advertisement. In buyer-seller networks, community detection facilitates better product recommendations. Unfortunately, reliability of community assignments is hindered by anomalous user behavior often observed as unfair self-promotion, or "fake" highly-connected accounts created to promote fraud. The present paper advocates a novel approach for jointly tracking communities while detecting such anomalous nodes in time-varying networks. By postulating edge creation as the result of mutual community participation by node pairs, a dynamic factor model with anomalous memberships captured through a sparse outlier matrix is put forth. Efficient tracking algorithms suitable for both online and decentralized operation are developed. Experiments conducted on both synthetic and real network time series successfully unveil underlying communities and anomalous nodes.


Attention-Based Models for Speech Recognition

arXiv.org Machine Learning

Recurrent sequence generators conditioned on input data through an attention mechanism have recently shown very good performance on a range of tasks in- cluding machine translation, handwriting synthesis and image caption gen- eration. We extend the attention-mechanism with features needed for speech recognition. We show that while an adaptation of the model used for machine translation in reaches a competitive 18.7% phoneme error rate (PER) on the TIMIT phoneme recognition task, it can only be applied to utterances which are roughly as long as the ones it was trained on. We offer a qualitative explanation of this failure and propose a novel and generic method of adding location-awareness to the attention mechanism to alleviate this issue. The new method yields a model that is robust to long inputs and achieves 18% PER in single utterances and 20% in 10-times longer (repeated) utterances. Finally, we propose a change to the at- tention mechanism that prevents it from concentrating too much on single frames, which further reduces PER to 17.6% level.