A Survey of Word Reordering in Statistical Machine Translation: Computational Models and Language Phenomena

Word reordering is one of the most difficult aspects of statistical machine translation (SMT), and an important factor of its quality and efficiency. Despite the vast amount of research published to date, the interest of the community in this problem has not decreased, and no single method appears to be strongly dominant across language pairs. Instead, the choice of the optimal approach for a new translation task still seems to be mostly driven by empirical trials. To orientate the reader in this vast and complex research area, we present a comprehensive survey of word reordering viewed as a statistical modeling challenge and as a natural language phenomenon. The survey describes in detail how word reordering is modeled within different string-based and tree-based SMT frameworks and as a stand-alone task, including systematic overviews of the literature in advanced reordering modeling. We then question why some approaches are more successful than others in different language pairs. We argue that, besides measuring the amount of reordering, it is important to understand which kinds of reordering occur in a given language pair. To this end, we conduct a qualitative analysis of word reordering phenomena in a diverse sample of language pairs, based on a large collection of linguistic knowledge. Empirical results in the SMT literature are shown to support the hypothesis that a few linguistic facts can be very useful to anticipate the reordering characteristics of a language pair and to select the SMT framework that best suits them.Comment: 44 pages, to appear in Computational Linguistic

Kernel methods in genomics and computational biology

Support vector machines and kernel methods are increasingly popular in genomics and computational biology, due to their good performance in real-world applications and strong modularity that makes them suitable to a wide range of problems, from the classification of tumors to the automatic annotation of proteins. Their ability to work in high dimension, to process non-vectorial data, and the natural framework they provide to integrate heterogeneous data are particularly relevant to various problems arising in computational biology. In this chapter we survey some of the most prominent applications published so far, highlighting the particular developments in kernel methods triggered by problems in biology, and mention a few promising research directions likely to expand in the future

A Survey on Metric Learning for Feature Vectors and Structured Data

The need for appropriate ways to measure the distance or similarity between data is ubiquitous in machine learning, pattern recognition and data mining, but handcrafting such good metrics for specific problems is generally difficult. This has led to the emergence of metric learning, which aims at automatically learning a metric from data and has attracted a lot of interest in machine learning and related fields for the past ten years. This survey paper proposes a systematic review of the metric learning literature, highlighting the pros and cons of each approach. We pay particular attention to Mahalanobis distance metric learning, a well-studied and successful framework, but additionally present a wide range of methods that have recently emerged as powerful alternatives, including nonlinear metric learning, similarity learning and local metric learning. Recent trends and extensions, such as semi-supervised metric learning, metric learning for histogram data and the derivation of generalization guarantees, are also covered. Finally, this survey addresses metric learning for structured data, in particular edit distance learning, and attempts to give an overview of the remaining challenges in metric learning for the years to come.Comment: Technical report, 59 pages. Changes in v2: fixed typos and improved presentation. Changes in v3: fixed typos. Changes in v4: fixed typos and new method

Continuous Action Recognition Based on Sequence Alignment

Continuous action recognition is more challenging than isolated recognition because classification and segmentation must be simultaneously carried out. We build on the well known dynamic time warping (DTW) framework and devise a novel visual alignment technique, namely dynamic frame warping (DFW), which performs isolated recognition based on per-frame representation of videos, and on aligning a test sequence with a model sequence. Moreover, we propose two extensions which enable to perform recognition concomitant with segmentation, namely one-pass DFW and two-pass DFW. These two methods have their roots in the domain of continuous recognition of speech and, to the best of our knowledge, their extension to continuous visual action recognition has been overlooked. We test and illustrate the proposed techniques with a recently released dataset (RAVEL) and with two public-domain datasets widely used in action recognition (Hollywood-1 and Hollywood-2). We also compare the performances of the proposed isolated and continuous recognition algorithms with several recently published methods

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This paper presents a new homology detection method MRFalign, consisting of three key components: 1) a Markov Random Fields (MRF) representation of a protein family; 2) a scoring function measuring similarity of two MRFs; and 3) an efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning two MRFs. Compared to HMM that can only model very short-range residue correlation, MRFs can model long-range residue interaction pattern and thus, encode information for the global 3D structure of a protein family. Consequently, MRF-MRF comparison for remote homology detection shall be much more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign outperforms several popular HMM or PSSM-based methods in terms of both alignment accuracy and remote homology detection and that MRFalign works particularly well for mainly beta proteins. For example, tested on the benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM succeed on 48% and 52% of proteins, respectively, at superfamily level, and on 15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign succeeds on 57.3% and 42.5% of proteins at superfamily and fold level, respectively. This study implies that long-range residue interaction patterns are very helpful for sequence-based homology detection. The software is available for download at http://raptorx.uchicago.edu/download/.Comment: Accepted by both RECOMB 2014 and PLOS Computational Biolog