COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment, and paired-end read LinkAge

The advent of next-generation sequencing (NGS) technologies enables researchers to sequence complex microbial communities directly from environment. Since assembly typically produces only genome fragments, also known as contigs, instead of entire genome, it is crucial to group them into operational taxonomic units (OTUs) for further taxonomic profiling and down-streaming functional analysis. OTU clustering is also referred to as binning. We present COCACOLA, a general framework automatically bin contigs into OTUs based upon sequence composition and coverage across multiple samples. The effectiveness of COCACOLA is demonstrated in both simulated and real datasets in comparison to state-of-art binning approaches such as CONCOCT, GroopM, MaxBin and MetaBAT. The superior performance of COCACOLA relies on two aspects. One is employing $L_{1}$ distance instead of Euclidean distance for better taxonomic identification during initialization. More importantly, COCACOLA takes advantage of both hard clustering and soft clustering by sparsity regularization. In addition, the COCACOLA framework seamlessly embraces customized knowledge to facilitate binning accuracy. In our study, we have investigated two types of additional knowledge, the co-alignment to reference genomes and linkage of contigs provided by paired-end reads, as well as the ensemble of both. We find that both co-alignment and linkage information further improve binning in the majority of cases. COCACOLA is scalable and faster than CONCOCT ,GroopM, MaxBin and MetaBAT. The software is available at https://github.com/younglululu/COCACOLAComment: 15 pages, 5 figures, 1 table paper accepted at the RECOMB-Seq 201

Information Extraction from Scientific Literature for Method Recommendation

As a research community grows, more and more papers are published each year. As a result there is increasing demand for improved methods for finding relevant papers, automatically understanding the key ideas and recommending potential methods for a target problem. Despite advances in search engines, it is still hard to identify new technologies according to a researcher's need. Due to the large variety of domains and extremely limited annotated resources, there has been relatively little work on leveraging natural language processing in scientific recommendation. In this proposal, we aim at making scientific recommendations by extracting scientific terms from a large collection of scientific papers and organizing the terms into a knowledge graph. In preliminary work, we trained a scientific term extractor using a small amount of annotated data and obtained state-of-the-art performance by leveraging large amount of unannotated papers through applying multiple semi-supervised approaches. We propose to construct a knowledge graph in a way that can make minimal use of hand annotated data, using only the extracted terms, unsupervised relational signals such as co-occurrence, and structural external resources such as Wikipedia. Latent relations between scientific terms can be learned from the graph. Recommendations will be made through graph inference for both observed and unobserved relational pairs.Comment: Thesis Proposal. arXiv admin note: text overlap with arXiv:1708.0607

Machine learning for metagenomics: methods and tools

Owing to the complexity and variability of metagenomic studies, modern machine learning approaches have seen increased usage to answer a variety of question encompassing the full range of metagenomic NGS data analysis. We review here the contribution of machine learning techniques for the field of metagenomics, by presenting known successful approaches in a unified framework. This review focuses on five important metagenomic problems: OTU-clustering, binning, taxonomic profling and assignment, comparative metagenomics and gene prediction. For each of these problems, we identify the most prominent methods, summarize the machine learning approaches used and put them into perspective of similar methods. We conclude our review looking further ahead at the challenge posed by the analysis of interactions within microbial communities and different environments, in a field one could call "integrative metagenomics"

A Joint Identification Approach for Argumentative Writing Revisions

Prior work on revision identification typically uses a pipeline method: revision extraction is first conducted to identify the locations of revisions and revision classification is then conducted on the identified revisions. Such a setting propagates the errors of the revision extraction step to the revision classification step. This paper proposes an approach that identifies the revision location and the revision type jointly to solve the issue of error propagation. It utilizes a sequence representation of revisions and conducts sequence labeling for revision identification. A mutation-based approach is utilized to update identification sequences. Results demonstrate that our proposed approach yields better performance on both revision location extraction and revision type classification compared to a pipeline baseline

An Attentive Survey of Attention Models

Attention Model has now become an important concept in neural networks that has been researched within diverse application domains. This survey provides a structured and comprehensive overview of the developments in modeling attention. In particular, we propose a taxonomy which groups existing techniques into coherent categories. We review salient neural architectures in which attention has been incorporated, and discuss applications in which modeling attention has shown a significant impact. We also describe how attention has been used to improve the interpretability of neural networks. Finally, we discuss some future research directions in attention. We hope this survey will provide a succinct introduction to attention models and guide practitioners while developing approaches for their applications.Comment: accepted to Transactions on Intelligent Systems and Technology(TIST); 33 page

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

PopIns: population-scale detection of novel sequence insertions

The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence insertions, insertions without similarity to a human reference genome, have received less attention than other types of SVs due to the computational challenges in their detection from short read sequencing data, which inherently involves de novo assembly. De novo assembly is not only computationally challenging, but also requires high-quality data. While the reads from a single individual may not always meet this requirement, using reads from multiple individuals can increase power to detect novel insertions. We have developed the program PopIns, which can discover and characterize non-reference insertions of 100 bp or longer on a population scale. In this paper, we describe the approach we implemented in PopIns. It takes as input a reads-to-reference alignment, assembles unaligned reads using a standard assembly tool, merges the contigs of different individuals into high-confidence sequences, anchors the merged sequences into the reference genome, and finally genotypes all individuals for the discovered insertions. Our tests on simulated data indicate that the merging step greatly improves the quality and reliability of predicted insertions and that PopIns shows significantly better recall and precision than the recent tool MindTheGap. Preliminary results on a data set of 305 Icelanders demonstrate the practicality of the new approach. The source code of PopIns is available from http://github.com/bkehr/popins.Comment: Presented at RECOMB-SEQ 201

Regulatory motif discovery using a population clustering evolutionary algorithm

This paper describes a novel evolutionary algorithm for regulatory motif discovery in DNA promoter sequences. The algorithm uses data clustering to logically distribute the evolving population across the search space. Mating then takes place within local regions of the population, promoting overall solution diversity and encouraging discovery of multiple solutions. Experiments using synthetic data sets have demonstrated the algorithm's capacity to find position frequency matrix models of known regulatory motifs in relatively long promoter sequences. These experiments have also shown the algorithm's ability to maintain diversity during search and discover multiple motifs within a single population. The utility of the algorithm for discovering motifs in real biological data is demonstrated by its ability to find meaningful motifs within muscle-specific regulatory sequences

Identification of functionally related enzymes by learning-to-rank methods

Enzyme sequences and structures are routinely used in the biological sciences as queries to search for functionally related enzymes in online databases. To this end, one usually departs from some notion of similarity, comparing two enzymes by looking for correspondences in their sequences, structures or surfaces. For a given query, the search operation results in a ranking of the enzymes in the database, from very similar to dissimilar enzymes, while information about the biological function of annotated database enzymes is ignored. In this work we show that rankings of that kind can be substantially improved by applying kernel-based learning algorithms. This approach enables the detection of statistical dependencies between similarities of the active cleft and the biological function of annotated enzymes. This is in contrast to search-based approaches, which do not take annotated training data into account. Similarity measures based on the active cleft are known to outperform sequence-based or structure-based measures under certain conditions. We consider the Enzyme Commission (EC) classification hierarchy for obtaining annotated enzymes during the training phase. The results of a set of sizeable experiments indicate a consistent and significant improvement for a set of similarity measures that exploit information about small cavities in the surface of enzymes

Recognizing Partial Biometric Patterns

Biometric recognition on partial captured targets is challenging, where only several partial observations of objects are available for matching. In this area, deep learning based methods are widely applied to match these partial captured objects caused by occlusions, variations of postures or just partial out of view in person re-identification and partial face recognition. However, most current methods are not able to identify an individual in case that some parts of the object are not obtainable, while the rest are specialized to certain constrained scenarios. To this end, we propose a robust general framework for arbitrary biometric matching scenarios without the limitations of alignment as well as the size of inputs. We introduce a feature post-processing step to handle the feature maps from FCN and a dictionary learning based Spatial Feature Reconstruction (SFR) to match different sized feature maps in this work. Moreover, the batch hard triplet loss function is applied to optimize the model. The applicability and effectiveness of the proposed method are demonstrated by the results from experiments on three person re-identification datasets (Market1501, CUHK03, DukeMTMC-reID), two partial person datasets (Partial REID and Partial iLIDS) and two partial face datasets (CASIA-NIR-Distance and Partial LFW), on which state-of-the-art performance is ensured in comparison with several state-of-the-art approaches. The code is released online and can be found on the website: https://github.com/lingxiao-he/Partial-Person-ReID.Comment: 13 pages, 11 figure