scholarly journals Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Morteza Pourreza Shahri ◽  
Indika Kahanda
Keyword(s):  
Ensemble Learning ◽  
Language Processing ◽  
Human Protein ◽  
Language Models ◽  
Convolutional Networks ◽  
Relationship Extraction ◽  
Novel Approach ◽  
Sentence Level ◽  
Human Proteins ◽  
Automated Tools

Abstract Background Identifying human protein-phenotype relationships has attracted researchers in bioinformatics and biomedical natural language processing due to its importance in uncovering rare and complex diseases. Since experimental validation of protein-phenotype associations is prohibitive, automated tools capable of accurately extracting these associations from the biomedical text are in high demand. However, while the manual annotation of protein-phenotype co-mentions required for training such models is highly resource-consuming, extracting millions of unlabeled co-mentions is straightforward. Results In this study, we propose a novel deep semi-supervised ensemble framework that combines deep neural networks, semi-supervised, and ensemble learning for classifying human protein-phenotype co-mentions with the help of unlabeled data. This framework allows the ability to incorporate an extensive collection of unlabeled sentence-level co-mentions of human proteins and phenotypes with a small labeled dataset to enhance overall performance. We develop PPPredSS, a prototype of our proposed semi-supervised framework that combines sophisticated language models, convolutional networks, and recurrent networks. Our experimental results demonstrate that the proposed approach provides a new state-of-the-art performance in classifying human protein-phenotype co-mentions by outperforming other supervised and semi-supervised counterparts. Furthermore, we highlight the utility of PPPredSS in powering a curation assistant system through case studies involving a group of biologists. Conclusions This article presents a novel approach for human protein-phenotype co-mention classification based on deep, semi-supervised, and ensemble learning. The insights and findings from this work have implications for biomedical researchers, biocurators, and the text mining community working on biomedical relationship extraction.

scholarly journals Predictions of Protein-Protein Interactions in Schistosoma Mansoni

2017 ◽  
Author(s):  
Javona White Bear ◽  
James H. McKerrow
Keyword(s):  
Schistosoma Mansoni ◽  
Language Processing ◽  
Protein Interactions ◽  
Species Interactions ◽  
Human Protein ◽  
Comparative Approach ◽  
Application Framework ◽  
Protein Protein Interactions ◽  
Protease Inhibition ◽  
Human Proteins

AbstractBackgroundSchistosoma mansoni invasion of the human host involves a variety of cross-species protein-protein interactions. The pathogen expresses a diverse arsenal of proteins that facilitate the breach of physical and biochemical barriers present in skin, evasion of the immune system, and digestion of human hemoglobin, allowing schistosomes to reside in the host for years. However, only a small number of specific interactions between S. mansoni and human proteins have been identified. We present and apply a protocol that generates testable predictions of S. mansoni-human protein interactions.MethodsIn this study, we first predict S. mansoni-human protein interactions based on similarity to known protein complexes. Putative interactions were then scored and assessed using several contextual filters, including the use of annotation automatically derived from literature using a simple natural language processing methodology. Our method predicted 7 out of the 10 previously known cross-species interactions.ConclusionsSeveral predictions that warrant experimental follow-up were presented and discussed, including interactions involving potential vaccine candidate antigens, protease inhibition, and immune evasion. The application framework provides an integrated methodology for investigation of host-pathogen interactions and an extensive source of orthogonal data for experimental analysis. We have made the predictions available online for community perusal.Author SummaryThe S. mansoni parasite is the etiological agent of the disease Schistomiasis. However, protein-protein interactions have been experimentally characterized that relate to pathogenesis and establishment of infection. As with many pathogens, the understanding of these interactions is a key component for the development of new vaccines. In this project, we have applied a computational whole-genome comparative approach to aid in the prediction of interactions between S. mansoni and human proteins and to identify important proteins involved in infection. The results of applying this method recapitulate several previously characterized interactions, as well as suggest additional ones as potential therapeutic targets.

scholarly journals On the Hierarchical Information in a Single Contextualised Word Representation (Student Abstract)

2020 ◽  
Vol 34 (10) ◽  
pp. 13917-13918
Author(s):  
Dean L. Slack ◽  
Mariann Hardey ◽  
Noura Al Moubayed
Keyword(s):  
Language Processing ◽  
Fine Tuning ◽  
Language Models ◽  
Linguistic Features ◽  
Widespread Application ◽  
Linear Classifiers ◽  
Sentence Level ◽  
Level Information ◽  
Word Representation ◽  
And Performance

Contextual word embeddings produced by neural language models, such as BERT or ELMo, have seen widespread application and performance gains across many Natural Language Processing tasks, suggesting rich linguistic features encoded in their representations. This work aims to investigate to what extent any linguistic hierarchical information is encoded into a single contextual embedding. Using labelled constituency trees, we train simple linear classifiers on top of single contextualised word representations for ancestor sentiment analysis tasks at multiple constituency levels of a sentence. To assess the presence of hierarchical information throughout the networks, the linear classifiers are trained using representations produced by each intermediate layer of BERT and ELMo variants. We show that with no fine-tuning, a single contextualised representation encodes enough syntactic and semantic sentence-level information to significantly outperform a non-contextual baseline for classifying 5-class sentiment of its ancestor constituents at multiple levels of the constituency tree. Additionally, we show that both LSTM and transformer architectures trained on similarly sized datasets achieve similar levels of performance on these tasks. Future work looks to expand the analysis to a wider range of NLP tasks and contextualisers.

scholarly journals Hierarchical Phoneme Classification for Improved Speech Recognition

2021 ◽  
Vol 11 (1) ◽  
pp. 428
Author(s):  
Donghoon Oh ◽  
Jeong-Sik Park ◽  
Ji-Hwan Kim ◽  
Gil-Jin Jang
Keyword(s):  
Speech Recognition ◽  
Language Processing ◽  
Confusion Matrix ◽  
Critical Factor ◽  
Recognition System ◽  
Classification Performance ◽  
Language Models ◽  
Successful Implementation ◽  
Phoneme Classification ◽  
Improved Performance

Speech recognition consists of converting input sound into a sequence of phonemes, then finding text for the input using language models. Therefore, phoneme classification performance is a critical factor for the successful implementation of a speech recognition system. However, correctly distinguishing phonemes with similar characteristics is still a challenging problem even for state-of-the-art classification methods, and the classification errors are hard to be recovered in the subsequent language processing steps. This paper proposes a hierarchical phoneme clustering method to exploit more suitable recognition models to different phonemes. The phonemes of the TIMIT database are carefully analyzed using a confusion matrix from a baseline speech recognition model. Using automatic phoneme clustering results, a set of phoneme classification models optimized for the generated phoneme groups is constructed and integrated into a hierarchical phoneme classification method. According to the results of a number of phoneme classification experiments, the proposed hierarchical phoneme group models improved performance over the baseline by 3%, 2.1%, 6.0%, and 2.2% for fricative, affricate, stop, and nasal sounds, respectively. The average accuracy was 69.5% and 71.7% for the baseline and proposed hierarchical models, showing a 2.2% overall improvement.

scholarly journals Efficient End-to-End Sentence-Level Lipreading with Temporal Convolutional Networks

2021 ◽  
Vol 11 (15) ◽  
pp. 6975
Author(s):  
Tao Zhang ◽  
Lun He ◽  
Xudong Li ◽  
Guoqing Feng
Keyword(s):  
Performance Improvement ◽  
State Of The Art ◽  
Error Rates ◽  
Convolutional Network ◽  
Convolutional Networks ◽  
Sentence Level ◽  
End To End ◽  
High Level ◽  
Improved Accuracy ◽  
Talking Face

Lipreading aims to recognize sentences being spoken by a talking face. In recent years, the lipreading method has achieved a high level of accuracy on large datasets and made breakthrough progress. However, lipreading is still far from being solved, and existing methods tend to have high error rates on the wild data and have the defects of disappearing training gradient and slow convergence. To overcome these problems, we proposed an efficient end-to-end sentence-level lipreading model, using an encoder based on a 3D convolutional network, ResNet50, Temporal Convolutional Network (TCN), and a CTC objective function as the decoder. More importantly, the proposed architecture incorporates TCN as a feature learner to decode feature. It can partly eliminate the defects of RNN (LSTM, GRU) gradient disappearance and insufficient performance, and this yields notable performance improvement as well as faster convergence. Experiments show that the training and convergence speed are 50% faster than the state-of-the-art method, and improved accuracy by 2.4% on the GRID dataset.

scholarly journals Automated Confirmation of Protein Annotation Using NLP and the UniProtKB Database

2020 ◽  
Vol 11 (1) ◽  
pp. 24
Author(s):  
Jin Tao ◽  
Kelly Brayton ◽  
Shira Broschat
Keyword(s):  
Language Processing ◽  
Fine Tuning ◽  
Support Vector ◽  
Protein Annotation ◽  
Computing Power ◽  
Journal Publication ◽  
Novel Approach ◽  
Uniprotkb Database ◽  
Public Repositories ◽  
Annotation Errors

Advances in genome sequencing technology and computing power have brought about the explosive growth of sequenced genomes in public repositories with a concomitant increase in annotation errors. Many protein sequences are annotated using computational analysis rather than experimental verification, leading to inaccuracies in annotation. Confirmation of existing protein annotations is urgently needed before misannotation becomes even more prevalent due to error propagation. In this work we present a novel approach for automatically confirming the existence of manually curated information with experimental evidence of protein annotation. Our ensemble learning method uses a combination of recurrent convolutional neural network, logistic regression, and support vector machine models. Natural language processing in the form of word embeddings is used with journal publication titles retrieved from the UniProtKB database. Importantly, we use recall as our most significant metric to ensure the maximum number of verifications possible; results are reported to a human curator for confirmation. Our ensemble model achieves 91.25% recall, 71.26% accuracy, 65.19% precision, and an F1 score of 76.05% and outperforms the Bidirectional Encoder Representations from Transformers for Biomedical Text Mining (BioBERT) model with fine-tuning using the same data.

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

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.

scholarly journals Using NLP in openEHR archetypes retrieval to promote interoperability: a feasibility study in China

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Bo Sun ◽  
Fei Zhang ◽  
Jing Li ◽  
Yicheng Yang ◽  
Xiaolin Diao ◽  
...  
Keyword(s):  
Information Sharing ◽  
Language Processing ◽  
Medical Information ◽  
Medical Professional ◽  
Semantic Interoperability ◽  
Medical Information System ◽  
Search Term ◽  
Search Terms ◽  
Novel Approach ◽  
Test Sets

Abstract Background With the development and application of medical information system, semantic interoperability is essential for accurate and advanced health-related computing and electronic health record (EHR) information sharing. The openEHR approach can improve semantic interoperability. One key improvement of openEHR is that it allows for the use of existing archetypes. The crucial problem is how to improve the precision and resolve ambiguity in the archetype retrieval. Method Based on the query expansion technology and Word2Vec model in Nature Language Processing (NLP), we propose to find synonyms as substitutes for original search terms in archetype retrieval. Test sets in different medical professional level are used to verify the feasibility. Result Applying the approach to each original search term (n = 120) in test sets, a total of 69,348 substitutes were constructed. Precision at 5 (P@5) was improved by 0.767, on average. For the best result, the P@5 was up to 0.975. Conclusions We introduce a novel approach that using NLP technology and corpus to find synonyms as substitutes for original search terms. Compared to simply mapping the element contained in openEHR to an external dictionary, this approach could greatly improve precision and resolve ambiguity in retrieval tasks. This is helpful to promote the application of openEHR and advance EHR information sharing.

Two New Large Corpora for Vietnamese Aspect-based Sentiment Analysis at Sentence Level

2021 ◽  
Vol 20 (4) ◽  
pp. 1-22
Author(s):  
Dang Van Thin ◽  
Ngan Luu-Thuy Nguyen ◽  
Tri Minh Truong ◽  
Lac Si Le ◽  
Duy Tin Vo
Keyword(s):  
Sentiment Analysis ◽  
Language Processing ◽  
Network Architectures ◽  
Low Resource ◽  
The Neural Network ◽  
Sentence Level ◽  
Push Forward ◽  
Polarity Classification ◽  
Learning Architectures ◽  
Single Approach

Aspect-based sentiment analysis has been studied in both research and industrial communities over recent years. For the low-resource languages, the standard benchmark corpora play an important role in the development of methods. In this article, we introduce two benchmark corpora with the largest sizes at sentence-level for two tasks: Aspect Category Detection and Aspect Polarity Classification in Vietnamese. Our corpora are annotated with high inter-annotator agreements for the restaurant and hotel domains. The release of our corpora would push forward the low-resource language processing community. In addition, we deploy and compare the effectiveness of supervised learning methods with a single and multi-task approach based on deep learning architectures. Experimental results on our corpora show that the multi-task approach based on BERT architecture outperforms the neural network architectures and the single approach. Our corpora and source code are published on this footnoted site. 1

scholarly journals Efficient Embedded Decoding of Neural Network Language Models in a Machine Translation System

2018 ◽  
Vol 28 (09) ◽  
pp. 1850007
Author(s):  
Francisco Zamora-Martinez ◽  
Maria Jose Castro-Bleda
Keyword(s):  
Neural Network ◽  
Machine Translation ◽  
Language Processing ◽  
Traditional Approach ◽  
Computational Cost ◽  
Integrated Approach ◽  
Language Models ◽  
Translation System ◽  
Neural Net ◽  
Network Language

Neural Network Language Models (NNLMs) are a successful approach to Natural Language Processing tasks, such as Machine Translation. We introduce in this work a Statistical Machine Translation (SMT) system which fully integrates NNLMs in the decoding stage, breaking the traditional approach based on [Formula: see text]-best list rescoring. The neural net models (both language models (LMs) and translation models) are fully coupled in the decoding stage, allowing to more strongly influence the translation quality. Computational issues were solved by using a novel idea based on memorization and smoothing of the softmax constants to avoid their computation, which introduces a trade-off between LM quality and computational cost. These ideas were studied in a machine translation task with different combinations of neural networks used both as translation models and as target LMs, comparing phrase-based and [Formula: see text]-gram-based systems, showing that the integrated approach seems more promising for [Formula: see text]-gram-based systems, even with nonfull-quality NNLMs.

scholarly journals A Cascaded Unsupervised Model for PoS Tagging

2021 ◽  
Vol 20 (1) ◽  
pp. 1-23
Author(s):  
Necva Bölücü ◽  
Burcu Can
Keyword(s):  
Linear Model ◽  
Language Processing ◽  
Bayesian Model ◽  
Linear Models ◽  
Syntactic Category ◽  
Semantic Parsing ◽  
Pos Tagging ◽  
Part Of Speech ◽  
Sentence Level ◽  
Log Linear

Part of speech (PoS) tagging is one of the fundamental syntactic tasks in Natural Language Processing, as it assigns a syntactic category to each word within a given sentence or context (such as noun, verb, adjective, etc.). Those syntactic categories could be used to further analyze the sentence-level syntax (e.g., dependency parsing) and thereby extract the meaning of the sentence (e.g., semantic parsing). Various methods have been proposed for learning PoS tags in an unsupervised setting without using any annotated corpora. One of the widely used methods for the tagging problem is log-linear models. Initialization of the parameters in a log-linear model is very crucial for the inference. Different initialization techniques have been used so far. In this work, we present a log-linear model for PoS tagging that uses another fully unsupervised Bayesian model to initialize the parameters of the model in a cascaded framework. Therefore, we transfer some knowledge between two different unsupervised models to leverage the PoS tagging results, where a log-linear model benefits from a Bayesian model’s expertise. We present results for Turkish as a morphologically rich language and for English as a comparably morphologically poor language in a fully unsupervised framework. The results show that our framework outperforms other unsupervised models proposed for PoS tagging.

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