scholarly journals MSCAT: A Machine Learning Assisted Catalog of Metabolomics Software Tools

Metabolites ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 678
Author(s):  
Jonathan Dekermanjian ◽  
Wladimir Labeikovsky ◽  
Debashis Ghosh ◽  
Katerina Kechris
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Conditional Random Fields ◽  
Short Term Memory ◽  
Named Entity Recognition ◽  
Software Tool ◽  
Software Tools ◽  
Entity Recognition ◽  
Metabolomics Data ◽  
Multiple Characteristics

The bottleneck for taking full advantage of metabolomics data is often the availability, awareness, and usability of analysis tools. Software tools specifically designed for metabolomics data are being developed at an increasing rate, with hundreds of available tools already in the literature. Many of these tools are open-source and freely available but are very diverse with respect to language, data formats, and stages in the metabolomics pipeline. To help mitigate the challenges of meeting the increasing demand for guidance in choosing analytical tools and coordinating the adoption of best practices for reproducibility, we have designed and built the MSCAT (Metabolomics Software CATalog) database of metabolomics software tools that can be sustainably and continuously updated. This database provides a survey of the landscape of available tools and can assist researchers in their selection of data analysis workflows for metabolomics studies according to their specific needs. We used machine learning (ML) methodology for the purpose of semi-automating the identification of metabolomics software tool names within abstracts. MSCAT searches the literature to find new software tools by implementing a Named Entity Recognition (NER) model based on a neural network model at the sentence level composed of a character-level convolutional neural network (CNN) combined with a bidirectional long-short-term memory (LSTM) layer and a conditional random fields (CRF) layer. The list of potential new tools (and their associated publication) is then forwarded to the database maintainer for the curation of the database entry corresponding to the tool. The end-user interface allows for filtering of tools by multiple characteristics as well as plotting of the aggregate tool data to monitor the metabolomics software landscape.

scholarly journals Information Extraction of Cybersecurity Concepts: An LSTM Approach

2019 ◽  
Vol 9 (19) ◽  
pp. 3945 ◽  
Author(s):  
Houssem Gasmi ◽  
Jannik Laval ◽  
Abdelaziz Bouras
Keyword(s):  
Neural Network ◽  
Domain Knowledge ◽  
Conditional Random Fields ◽  
Short Term Memory ◽  
Network Models ◽  
Relation Extraction ◽  
Entity Recognition ◽  
Feature Engineering ◽  
Neural Network Models ◽  
Feature Based

Extracting cybersecurity entities and the relationships between them from online textual resources such as articles, bulletins, and blogs and converting these resources into more structured and formal representations has important applications in cybersecurity research and is valuable for professional practitioners. Previous works to accomplish this task were mainly based on utilizing feature-based models. Feature-based models are time-consuming and need labor-intensive feature engineering to describe the properties of entities, domain knowledge, entity context, and linguistic characteristics. Therefore, to alleviate the need for feature engineering, we propose the usage of neural network models, specifically the long short-term memory (LSTM) models to accomplish the tasks of Named Entity Recognition (NER) and Relation Extraction (RE). We evaluated the proposed models on two tasks. The first task is performing NER and evaluating the results against the state-of-the-art Conditional Random Fields (CRFs) method. The second task is performing RE using three LSTM models and comparing their results to assess which model is more suitable for the domain of cybersecurity. The proposed models achieved competitive performance with less feature-engineering work. We demonstrate that exploiting neural network models in cybersecurity text mining is effective and practical.

scholarly journals Innovative Deep Neural Network Modeling for Fine-Grained Chinese Entity Recognition

Electronics ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1001 ◽  
Author(s):  
Jingang Liu ◽  
Chunhe Xia ◽  
Haihua Yan ◽  
Wenjing Xu
Keyword(s):  
Neural Network ◽  
Language Processing ◽  
Short Term Memory ◽  
Named Entity Recognition ◽  
Training Model ◽  
Entity Recognition ◽  
Coarse Grained ◽  
Neural Network Modeling ◽  
Fine Grained ◽  
Named Entity

Named entity recognition (NER) is a basic but crucial task in the field of natural language processing (NLP) and big data analysis. The recognition of named entities based on Chinese is more complicated and difficult than English, which makes the task of NER in Chinese more challenging. In particular, fine-grained named entity recognition is more challenging than traditional named entity recognition tasks, mainly because fine-grained tasks have higher requirements for the ability of automatic feature extraction and information representation of deep neural models. In this paper, we propose an innovative neural network model named En2BiLSTM-CRF to improve the effect of fine-grained Chinese entity recognition tasks. This proposed model including the initial encoding layer, the enhanced encoding layer, and the decoding layer combines the advantages of pre-training model encoding, dual bidirectional long short-term memory (BiLSTM) networks, and a residual connection mechanism. Hence, it can encode information multiple times and extract contextual features hierarchically. We conducted sufficient experiments on two representative datasets using multiple important metrics and compared them with other advanced baselines. We present promising results showing that our proposed En2BiLSTM-CRF has better performance as well as better generalization ability in both fine-grained and coarse-grained Chinese entity recognition tasks.

scholarly journals Ontology-Based Healthcare Named Entity Recognition from Twitter Messages Using a Recurrent Neural Network Approach

2019 ◽  
Vol 16 (19) ◽  
pp. 3628 ◽  
Author(s):  
Erdenebileg Batbaatar ◽  
Keun Ho Ryu
Keyword(s):  
Neural Network ◽  
Recurrent Neural Network ◽  
Adverse Drug Events ◽  
Viterbi Algorithm ◽  
Short Term Memory ◽  
Conditional Random Field ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Named Entity ◽  
Health Related

Named Entity Recognition (NER) in the healthcare domain involves identifying and categorizing disease, drugs, and symptoms for biosurveillance, extracting their related properties and activities, and identifying adverse drug events appearing in texts. These tasks are important challenges in healthcare. Analyzing user messages in social media networks such as Twitter can provide opportunities to detect and manage public health events. Twitter provides a broad range of short messages that contain interesting information for information extraction. In this paper, we present a Health-Related Named Entity Recognition (HNER) task using healthcare-domain ontology that can recognize health-related entities from large numbers of user messages from Twitter. For this task, we employ a deep learning architecture which is based on a recurrent neural network (RNN) with little feature engineering. To achieve our goal, we collected a large number of Twitter messages containing health-related information, and detected biomedical entities from the Unified Medical Language System (UMLS). A bidirectional long short-term memory (BiLSTM) model learned rich context information, and a convolutional neural network (CNN) was used to produce character-level features. The conditional random field (CRF) model predicted a sequence of labels that corresponded to a sequence of inputs, and the Viterbi algorithm was used to detect health-related entities from Twitter messages. We provide comprehensive results giving valuable insights for identifying medical entities in Twitter for various applications. The BiLSTM-CRF model achieved a precision of 93.99%, recall of 73.31%, and F1-score of 81.77% for disease or syndrome HNER; a precision of 90.83%, recall of 81.98%, and F1-score of 87.52% for sign or symptom HNER; and a precision of 94.85%, recall of 73.47%, and F1-score of 84.51% for pharmacologic substance named entities. The ontology-based manual annotation results show that it is possible to perform high-quality annotation despite the complexity of medical terminology and the lack of context in tweets.

An Experimental Study of Hybrid Machine Learning Models for Extracting Named Entities

10.29007/dp5m ◽  
2019 ◽  
Author(s):  
Lei Jiang ◽  
Elena Bolshakova
Keyword(s):  
Neural Network ◽  
Conditional Random Fields ◽  
Named Entity Recognition ◽  
Network Models ◽  
Entity Recognition ◽  
Neural Network Models ◽  
Named Entities ◽  
Hybrid Neural Network ◽  
Named Entity ◽  
Two Hybrid

The paper describes two hybrid neural network models for named entity recognition (NER) in texts, as well as results of experiments with them. The first model, namely Bi-LSTM-CRF, is known and used for NER, while the other model named Gated-CNN- CRF is proposed in this work. It combines convolutional neural network (CNN), gated linear units, and conditional random fields (CRF). Both models were tested for NER on three different language datasets, for English, Russian, and Chinese. All resulted scores of precision, recall and F1-measure for both models are close to the state-of-the-art for NER, and for the English dataset CoNLL-2003, Gated-CNN-CRF model achieves 92.66 of F1-measure, outperforming the known result.

A Software Tool for Biomedical Information Extraction (And Beyond)

2011 ◽  
pp. 975-985
Author(s):  
Burr Settles
Keyword(s):  
Open Source ◽  
Language Processing ◽  
Conditional Random Fields ◽  
Named Entity Recognition ◽  
Software Tool ◽  
Cell Types ◽  
Entity Recognition ◽  
Named Entity ◽  
Software Distribution ◽  
Classification Information

ABNER (A Biomedical Named Entity Recognizer) is an open-source software tool for text mining in the molecular biology literature. It processes unstructured biomedical documents in order to discover and annotate mentions of genes, proteins, cell types, and other entities of interest. This task, known as named entity recognition (NER), is an important first step for many larger information management goals in biomedicine, namely extraction of biochemical relationships, document classification, information retrieval, and the like. To accomplish this task, ABNER uses state-of-the-art machine learning models for sequence labeling called conditional random fields (CRFs). The software distribution comes bundled with two models that are pre-trained on standard evaluation corpora. ABNER can run as a stand-alone application with a graphical user interface, or be accessed as a Java API allowing it to be re-trained with new labeled corpora and incorporated into other, higher-level applications. This chapter describes the software and its features, presents an overview of the underlying technology, and provides a discussion of some of the more advanced natural language processing systems for which ABNER has been used as a component. ABNER is open-source and freely available from http://pages. cs.wisc.edu/~bsettles/abner/

scholarly journals Viability of Neural Networks for Core Technologies for Resource-Scarce Languages

Information ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 41
Author(s):  
Melinda Loubser ◽  
Martin J. Puttkammer
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Neural Networks ◽  
South African ◽  
Language Processing ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Neural Network Models ◽  
African Languages ◽  
Pos Tagging

In this paper, the viability of neural network implementations of core technologies (the focus of this paper is on text technologies) for 10 resource-scarce South African languages is evaluated. Neural networks are increasingly being used in place of other machine learning methods for many natural language processing tasks with good results. However, in the South African context, where most languages are resource-scarce, very little research has been done on neural network implementations of core language technologies. In this paper, we address this gap by evaluating neural network implementations of four core technologies for ten South African languages. The technologies we address are part of speech tagging, named entity recognition, compound analysis and lemmatization. Neural architectures that performed well on similar tasks in other settings were implemented for each task and the performance was assessed in comparison with currently used machine learning implementations of each technology. The neural network models evaluated perform better than the baselines for compound analysis, are viable and comparable to the baseline on most languages for POS tagging and NER, and are viable, but not on par with the baseline, for Afrikaans lemmatization.

scholarly journals Bidirectional Recurrent Neural Network Approach for Arabic Named Entity Recognition

2018 ◽  
Vol 10 (12) ◽  
pp. 123 ◽  
Author(s):  
Mohammed Ali ◽  
Guanzheng Tan ◽  
Aamir Hussain
Keyword(s):  
Neural Network ◽  
Language Processing ◽  
Recurrent Neural Network ◽  
Short Term Memory ◽  
Named Entity Recognition ◽  
Recognition Task ◽  
Word Embedding ◽  
Entity Recognition ◽  
Named Entity ◽  
Lstm Network

Recurrent neural network (RNN) has achieved remarkable success in sequence labeling tasks with memory requirement. RNN can remember previous information of a sequence and can thus be used to solve natural language processing (NLP) tasks. Named entity recognition (NER) is a common task of NLP and can be considered a classification problem. We propose a bidirectional long short-term memory (LSTM) model for this entity recognition task of the Arabic text. The LSTM network can process sequences and relate to each part of it, which makes it useful for the NER task. Moreover, we use pre-trained word embedding to train the inputs that are fed into the LSTM network. The proposed model is evaluated on a popular dataset called “ANERcorp.” Experimental results show that the model with word embedding achieves a high F-score measure of approximately 88.01%.

scholarly journals Evaluating Named-Entity Recognition approaches in plant molecular biology

2018 ◽  
Author(s):  
Huy Do ◽  
Khoat Than ◽  
Pierre Larmande
Keyword(s):  
Text Mining ◽  
Molecular Biology ◽  
Conditional Random Fields ◽  
Short Term Memory ◽  
Named Entity Recognition ◽  
Plant Molecular Biology ◽  
Entity Recognition ◽  
Biological Knowledge ◽  
Phenotypic Traits ◽  
Accurate Analysis

AbstractText mining research is becoming an important topic in biology with the aim to extract biological entities from scientific papers in order to extend the biological knowledge. However, few thorough studies on text mining and applications are developed for plant molecular biology data, especially rice, thus resulting a lack of datasets available to train models able to detect entities such as genes, proteins and phenotypic traits. Since there is rare benchmarks for rice, we have to face various difficulties in exploiting advanced machine learning methods for accurate analysis of rice bibliography. In this article, we developed a new training datasets (Oryzabase) as the benchmark. Then, we evaluated the performance of several current approaches to find a methodology with the best results and assigned it as the state of the art method for our own technique in the future. We applied Name Entities Recognition (NER) tagger, which is built from a Long Short Term Memory (LSTM) model, and combined with Conditional Random Fields (CRFs) to extract information of rice genes and proteins. We analyzed the performance of LSTM-CRF when applying to the Oryzabase dataset and improved the results up to 86% in F1. We found that on average, the result from LSTM-CRF is more exploitable with the new benchmark.

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