GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography

Abstract Summary We present GeoBoost2, a natural language-processing pipeline for extracting the location of infected hosts for enriching metadata in nucleotide sequences repositories like National Center of Biotechnology Information’s GenBank for downstream analysis including phylogeography and genomic epidemiology. The increasing number of pathogen sequences requires complementary information extraction methods for focused research, including surveillance within countries and between borders. In this article, we describe the enhancements from our earlier release including improvement in end-to-end extraction performance and speed, availability of a fully functional web-interface and state-of-the-art methods for location extraction using deep learning. Availability and implementation Application is freely available on the web at https://zodo.asu.edu/geoboost2. Source code, usage examples and annotated data for GeoBoost2 is freely available at https://github.com/ZooPhy/geoboost2. Supplementary information Supplementary data are available at Bioinformatics online.

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Unsupervised Keyphrase Extraction for Web Pages

Multimodal Technologies and Interaction ◽

10.3390/mti3030058 ◽

2019 ◽

Vol 3 (3) ◽

pp. 58 ◽

Cited By ~ 1

Author(s):

Tim Haarman ◽

Bastiaan Zijlema ◽

Marco Wiering

Keyword(s):

Language Processing ◽

State Of The Art ◽

Structural Information ◽

Extraction Methods ◽

Web Pages ◽

Keyphrase Extraction ◽

Text Documents ◽

Normal Text ◽

Textual Data ◽

Novel Method

Keyphrase extraction is an important part of natural language processing (NLP) research, although little research is done in the domain of web pages. The World Wide Web contains billions of pages that are potentially interesting for various NLP tasks, yet it remains largely untouched in scientific research. Current research is often only applied to clean corpora such as abstracts and articles from academic journals or sets of scraped texts from a single domain. However, textual data from web pages differ from normal text documents, as it is structured using HTML elements and often consists of many small fragments. These elements are furthermore used in a highly inconsistent manner and are likely to contain noise. We evaluated the keyphrases extracted by several state-of-the-art extraction methods and found that they did not transfer well to web pages. We therefore propose WebEmbedRank, an adaptation of a recently proposed extraction method that can make use of structural information in web pages in a robust manner. We compared this novel method to other baselines and state-of-the-art methods using a manually annotated dataset and found that WebEmbedRank achieved significant improvements over existing extraction methods on web pages.

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Towards relation extraction from Arabic text: a review

International Robotics & Automation Journal ◽

10.15406/iratj.2019.05.00195 ◽

2019 ◽

Vol 5 (5) ◽

pp. 212-215

Author(s):

Abeer AlArfaj

Keyword(s):

Language Processing ◽

Question Answering ◽

State Of The Art ◽

Relation Extraction ◽

Arabic Language ◽

Extraction Methods ◽

The State ◽

Semantic Relations ◽

Arabic Text ◽

Taxonomic Relation

Semantic relation extraction is an important component of ontologies that can support many applications e.g. text mining, question answering, and information extraction. However, extracting semantic relations between concepts is not trivial and one of the main challenges in Natural Language Processing (NLP) Field. The Arabic language has complex morphological, grammatical, and semantic aspects since it is a highly inflectional and derivational language, which makes task even more challenging. In this paper, we present a review of the state of the art for relation extraction from texts, addressing the progress and difficulties in this field. We discuss several aspects related to this task, considering the taxonomic and non-taxonomic relation extraction methods. Majority of relation extraction approaches implement a combination of statistical and linguistic techniques to extract semantic relations from text. We also give special attention to the state of the work on relation extraction from Arabic texts, which need further progress.

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UDSMProt: universal deep sequence models for protein classification

Bioinformatics ◽

10.1093/bioinformatics/btaa003 ◽

2020 ◽

Vol 36 (8) ◽

pp. 2401-2409 ◽

Cited By ~ 9

Author(s):

Nils Strodthoff ◽

Patrick Wagner ◽

Markus Wenzel ◽

Wojciech Samek

Keyword(s):

Language Processing ◽

State Of The Art ◽

Fine Tuning ◽

Supplementary Information ◽

Protein Classification ◽

Class Prediction ◽

Scoring Matrices ◽

Modern Natural ◽

Protein Properties ◽

Classification Tasks

Abstract Motivation Inferring the properties of a protein from its amino acid sequence is one of the key problems in bioinformatics. Most state-of-the-art approaches for protein classification are tailored to single classification tasks and rely on handcrafted features, such as position-specific-scoring matrices from expensive database searches. We argue that this level of performance can be reached or even be surpassed by learning a task-agnostic representation once, using self-supervised language modeling, and transferring it to specific tasks by a simple fine-tuning step. Results We put forward a universal deep sequence model that is pre-trained on unlabeled protein sequences from Swiss-Prot and fine-tuned on protein classification tasks. We apply it to three prototypical tasks, namely enzyme class prediction, gene ontology prediction and remote homology and fold detection. The proposed method performs on par with state-of-the-art algorithms that were tailored to these specific tasks or, for two out of three tasks, even outperforms them. These results stress the possibility of inferring protein properties from the sequence alone and, on more general grounds, the prospects of modern natural language processing methods in omics. Moreover, we illustrate the prospects for explainable machine learning methods in this field by selected case studies. Availability and implementation Source code is available under https://github.com/nstrodt/UDSMProt. Supplementary information Supplementary data are available at Bioinformatics online.

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BloodGen3Module: Blood transcriptional module repertoire analysis and visualization using R

Bioinformatics ◽

10.1093/bioinformatics/btab121 ◽

2021 ◽

Author(s):

Darawan Rinchai ◽

Jessica Roelands ◽

Mohammed Toufiq ◽

Wouter Hendrickx ◽

Matthew C Altman ◽

...

Keyword(s):

Transcript Abundance ◽

R Package ◽

Supplementary Information ◽

Illustrative Case ◽

Bioinformatic Tools ◽

Transcriptional Module ◽

Wide Range ◽

Downstream Analysis ◽

Computing Module ◽

Parallel Workflow

Abstract Motivation We previously described the construction and characterization of generic and reusable blood transcriptional module repertoires. More recently we released a third iteration (“BloodGen3” module repertoire) that comprises 382 functionally annotated gene sets (modules) and encompasses 14,168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires. Results We have developed and describe here a R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states. Availability The BloodGen3Module package and documentation are freely available from Github: https://github.com/Drinchai/BloodGen3Module Supplementary information Supplementary data are available at Bioinformatics online.

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Report on the 4th Joint Workshop on Bibliometric-Enhanced Information Retrieval and Natural Language Processing for Digital Libraries at SIGIR 2019

ACM SIGIR Forum ◽

10.1145/3458553.3458554 ◽

2019 ◽

Vol 53 (2) ◽

pp. 3-10

Author(s):

Muthu Kumar Chandrasekaran ◽

Philipp Mayr

Keyword(s):

Information Retrieval ◽

Natural Language Processing ◽

Natural Language ◽

Research And Development ◽

Language Processing ◽

Digital Libraries ◽

State Of The Art ◽

Shared Task ◽

Processing Information ◽

Joint Workshop

The 4 th joint BIRNDL workshop was held at the 42nd ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR 2019) in Paris, France. BIRNDL 2019 intended to stimulate IR researchers and digital library professionals to elaborate on new approaches in natural language processing, information retrieval, scientometrics, and recommendation techniques that can advance the state-of-the-art in scholarly document understanding, analysis, and retrieval at scale. The workshop incorporated different paper sessions and the 5 th edition of the CL-SciSumm Shared Task.

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Learning emotional word embeddings for sentiment analysis

Journal of Intelligent & Fuzzy Systems ◽

10.3233/jifs-201993 ◽

2021 ◽

pp. 1-13

Author(s):

Qingtian Zeng ◽

Xishi Zhao ◽

Xiaohui Hu ◽

Hua Duan ◽

Zhongying Zhao ◽

...

Keyword(s):

Sentiment Analysis ◽

Language Processing ◽

State Of The Art ◽

Research Problem ◽

Emotional Word ◽

Classification Model ◽

Data Sets ◽

Word Embeddings ◽

Real World Data ◽

Text Documents

Word embeddings have been successfully applied in many natural language processing tasks due to its their effectiveness. However, the state-of-the-art algorithms for learning word representations from large amounts of text documents ignore emotional information, which is a significant research problem that must be addressed. To solve the above problem, we propose an emotional word embedding (EWE) model for sentiment analysis in this paper. This method first applies pre-trained word vectors to represent document features using two different linear weighting methods. Then, the resulting document vectors are input to a classification model and used to train a text sentiment classifier, which is based on a neural network. In this way, the emotional polarity of the text is propagated into the word vectors. The experimental results on three kinds of real-world data sets demonstrate that the proposed EWE model achieves superior performances on text sentiment prediction, text similarity calculation, and word emotional expression tasks compared to other state-of-the-art models.

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Towards corpus and model: Hierarchical structured-attention-based features for Indonesian named entity recognition

Journal of Intelligent & Fuzzy Systems ◽

10.3233/jifs-202286 ◽

2021 ◽

pp. 1-12

Author(s):

Yingwen Fu ◽

Nankai Lin ◽

Xiaotian Lin ◽

Shengyi Jiang

Keyword(s):

Language Processing ◽

State Of The Art ◽

Named Entity Recognition ◽

Entity Recognition ◽

Language Models ◽

Neural Models ◽

Performance Models ◽

Named Entity ◽

High Resource ◽

Benchmark Datasets

Named entity recognition (NER) is fundamental to natural language processing (NLP). Most state-of-the-art researches on NER are based on pre-trained language models (PLMs) or classic neural models. However, these researches are mainly oriented to high-resource languages such as English. While for Indonesian, related resources (both in dataset and technology) are not yet well-developed. Besides, affix is an important word composition for Indonesian language, indicating the essentiality of character and token features for token-wise Indonesian NLP tasks. However, features extracted by currently top-performance models are insufficient. Aiming at Indonesian NER task, in this paper, we build an Indonesian NER dataset (IDNER) comprising over 50 thousand sentences (over 670 thousand tokens) to alleviate the shortage of labeled resources in Indonesian. Furthermore, we construct a hierarchical structured-attention-based model (HSA) for Indonesian NER to extract sequence features from different perspectives. Specifically, we use an enhanced convolutional structure as well as an enhanced attention structure to extract deeper features from characters and tokens. Experimental results show that HSA establishes competitive performance on IDNER and three benchmark datasets.

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CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

Bioinformatics ◽

10.1093/bioinformatics/btaa1047 ◽

2020 ◽

Author(s):

Matteo Chiara ◽

Federico Zambelli ◽

Marco Antonio Tangaro ◽

Pietro Mandreoli ◽

David S Horner ◽

...

Keyword(s):

Functional Annotation ◽

Ad Hoc ◽

State Of The Art ◽

Supplementary Information ◽

Genomic Sequences ◽

Supplementary Data ◽

Evolutionary Patterns ◽

Genomic Variants ◽

Art Methods ◽

Available Resources

Abstract Summary While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2. Availabilityand implementation Galaxy http://corgat.cloud.ba.infn.it/galaxy; software: https://github.com/matteo14c/CorGAT/tree/Revision_V1; docker: https://hub.docker.com/r/laniakeacloud/galaxy_corgat. Supplementary information Supplementary data are available at Bioinformatics online.

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New Multi-View Classification Method with Uncertain Data

ACM Transactions on Knowledge Discovery from Data ◽

10.1145/3458282 ◽

2021 ◽

Vol 16 (1) ◽

pp. 1-23

Author(s):

Bo Liu ◽

Haowen Zhong ◽

Yanshan Xiao

Keyword(s):

Learning Strategy ◽

State Of The Art ◽

Uncertain Data ◽

Real Life ◽

Support Vector ◽

Classification Methods ◽

Complementary Information ◽

Novel Approach ◽

Svm Model ◽

Iterative Framework

Multi-view classification aims at designing a multi-view learning strategy to train a classifier from multi-view data, which are easily collected in practice. Most of the existing works focus on multi-view classification by assuming the multi-view data are collected with precise information. However, we always collect the uncertain multi-view data due to the collection process is corrupted with noise in real-life application. In this case, this article proposes a novel approach, called uncertain multi-view learning with support vector machine (UMV-SVM) to cope with the problem of multi-view learning with uncertain data. The method first enforces the agreement among all the views to seek complementary information of multi-view data and takes the uncertainty of the multi-view data into consideration by modeling reachability area of the noise. Then it proposes an iterative framework to solve the proposed UMV-SVM model such that we can obtain the multi-view classifier for prediction. Extensive experiments on real-life datasets have shown that the proposed UMV-SVM can achieve a better performance for uncertain multi-view classification in comparison to the state-of-the-art multi-view classification methods.

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Fast detection of differential chromatin domains with SCIDDO

Bioinformatics ◽

10.1093/bioinformatics/btaa960 ◽

2020 ◽

Author(s):

Peter Ebert ◽

Marcel H Schulz

Keyword(s):

Differentially Expressed Genes ◽

Differentially Expressed ◽

Chromatin State ◽

Supplementary Information ◽

Differential Analysis ◽

Chromatin Domains ◽

Chromatin Dynamics ◽

Histone Marks ◽

Chromatin Immunoprecipitation Sequencing ◽

Downstream Analysis

Abstract Motivation The generation of genome-wide maps of histone modifications using chromatin immunoprecipitation sequencing (ChIP-seq) is a standard approach to dissect the complexity of the epigenome. Interpretation and differential analysis of histone datasets remains challenging due to regulatory meaningful co-occurrences of histone marks and their difference in genomic spread. To ease interpretation, chromatin state segmentation maps are a commonly employed abstraction combining individual histone marks. We developed the tool SCIDDO as a fast, flexible, and statistically sound method for the differential analysis of chromatin state segmentation maps. Results We demonstrate the utility of SCIDDO in a comparative analysis that identifies differential chromatin domains (DCD) in various regulatory contexts and with only moderate computational resources. We show that the identified DCDs correlate well with observed changes in gene expression and can recover a substantial number of differentially expressed genes. We showcase SCIDDO’s ability to directly interrogate chromatin dynamics such as enhancer switches in downstream analysis, which simplifies exploring specific questions about regulatory changes in chromatin. By comparing SCIDDO to competing methods, we provide evidence that SCIDDO’s performance in identifying differentially expressed genes (DEG) via differential chromatin marking is more stable across a range of cell-type comparisons and parameter cut-offs. Availability The SCIDDO source code is openly available under github.com/ptrebert/sciddo Supplementary information Supplementary data are available at Bioinformatics online.

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