scholarly journals Identification of Bacteriophages Using Deep Representation Model with Pre-training

2021 ◽  
Author(s):  
Zeheng Bai ◽  
Yao-zhong Zhang ◽  
Satoru Miyano ◽  
Rui Yamaguchi ◽  
Satoshi Uematsu ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Deep Learning ◽  
Sequence Similarity ◽  
Representation Learning ◽  
Learning Model ◽  
Third Party ◽  
Knowledge Representations ◽  
Learning Framework ◽  
Advantages And Disadvantages ◽  
Alignment Free

Bacteriophages/Phages are viruses that infect and replicate within bacteria and archaea. Antibiotic resistance is one of the biggest threats to global health. The therapeutic use of bacteriophages provides another potential solution for solving antibiotic resistance. To develop phage therapies, the identification of phages from metagenome sequences is the fundamental step. Currently, several methods have been developed for identifying phages. These methods can be categorized into two types: database-based methods and alignment-free methods. The database-based approach, such as VIBRANT, utilizes existing databases and compares sequence similarity between candidates and those in the databases. The alignment-free method, such as Seeker and DeepVirFinder, uses deep learning models to directly predict phages based on nucleotide sequences. Both approaches have their advantages and disadvantages. In this work, we propose using a deep representation learning model with pre-training to integrate the database-based and non-alignment-based methods (we call it INHERIT). The pre-training is used as an alternative way for acquiring knowledge representations from existing databases, while the BERT-style deep learning framework retains the advantage of alignment-free methods. We compared the proposed method with VIBRANT and Seeker on a third-party benchmark dataset. Our experiments show that INHERIT achieves better performance than the database-based approach and the alignment-free method, with the best F1-score of 0.9868. Meanwhile, we demonstrated that using pre-trained models helps to improve the non-alignment deep learning model further.

scholarly journals HMD-ARG: hierarchical multi-task deep learning for annotating antibiotic resistance genes

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Yu Li ◽  
Zeling Xu ◽  
Wenkai Han ◽  
Huiluo Cao ◽  
Ramzan Umarov ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Deep Learning ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Third Party ◽  
Superior Performance ◽  
Beta Lactamase ◽  
Learning Framework ◽  
Sequence Encoding ◽  
Global Threat

Abstract Background The spread of antibiotic resistance has become one of the most urgent threats to global health, which is estimated to cause 700,000 deaths each year globally. Its surrogates, antibiotic resistance genes (ARGs), are highly transmittable between food, water, animal, and human to mitigate the efficacy of antibiotics. Accurately identifying ARGs is thus an indispensable step to understanding the ecology, and transmission of ARGs between environmental and human-associated reservoirs. Unfortunately, the previous computational methods for identifying ARGs are mostly based on sequence alignment, which cannot identify novel ARGs, and their applications are limited by currently incomplete knowledge about ARGs. Results Here, we propose an end-to-end Hierarchical Multi-task Deep learning framework for ARG annotation (HMD-ARG). Taking raw sequence encoding as input, HMD-ARG can identify, without querying against existing sequence databases, multiple ARG properties simultaneously, including if the input protein sequence is an ARG, and if so, what antibiotic family it is resistant to, what resistant mechanism the ARG takes, and if the ARG is an intrinsic one or acquired one. In addition, if the predicted antibiotic family is beta-lactamase, HMD-ARG further predicts the subclass of beta-lactamase that the ARG is resistant to. Comprehensive experiments, including cross-fold validation, third-party dataset validation in human gut microbiota, wet-experimental functional validation, and structural investigation of predicted conserved sites, demonstrate not only the superior performance of our method over the state-of-art methods, but also the effectiveness and robustness of the proposed method. Conclusions We propose a hierarchical multi-task method, HMD-ARG, which is based on deep learning and can provide detailed annotations of ARGs from three important aspects: resistant antibiotic class, resistant mechanism, and gene mobility. We believe that HMD-ARG can serve as a powerful tool to identify antibiotic resistance genes and, therefore mitigate their global threat. Our method and the constructed database are available at http://www.cbrc.kaust.edu.sa/HMDARG/.

BEHRT-HF: an interpretable transformer-based, deep learning model for prediction of incident heart failure

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
S Rao ◽  
Y Li ◽  
R Ramakrishnan ◽  
A Hassaine ◽  
D Canoy ◽  
...  
Keyword(s):  
Heart Failure ◽  
Deep Learning ◽  
State Of The Art ◽  
Failure Prediction ◽  
Predictive Performance ◽  
Learning Model ◽  
Learning Framework ◽  
Incident Heart Failure ◽  
Ablation Study ◽  
Deep Learning Model

Abstract Background/Introduction Predicting incident heart failure has been challenging. Deep learning models when applied to rich electronic health records (EHR) offer some theoretical advantages. However, empirical evidence for their superior performance is limited and they remain commonly uninterpretable, hampering their wider use in medical practice. Purpose We developed a deep learning framework for more accurate and yet interpretable prediction of incident heart failure. Methods We used longitudinally linked EHR from practices across England, involving 100,071 patients, 13% of whom had been diagnosed with incident heart failure during follow-up. We investigated the predictive performance of a novel transformer deep learning model, “Transformer for Heart Failure” (BEHRT-HF), and validated it using both an external held-out dataset and an internal five-fold cross-validation mechanism using area under receiver operating characteristic (AUROC) and area under the precision recall curve (AUPRC). Predictor groups included all outpatient and inpatient diagnoses within their temporal context, medications, age, and calendar year for each encounter. By treating diagnoses as anchors, we alternatively removed different modalities (ablation study) to understand the importance of individual modalities to the performance of incident heart failure prediction. Using perturbation-based techniques, we investigated the importance of associations between selected predictors and heart failure to improve model interpretability. Results BEHRT-HF achieved high accuracy with AUROC 0.932 and AUPRC 0.695 for external validation, and AUROC 0.933 (95% CI: 0.928, 0.938) and AUPRC 0.700 (95% CI: 0.682, 0.718) for internal validation. Compared to the state-of-the-art recurrent deep learning model, RETAIN-EX, BEHRT-HF outperformed it by 0.079 and 0.030 in terms of AUPRC and AUROC. Ablation study showed that medications were strong predictors, and calendar year was more important than age. Utilising perturbation, we identified and ranked the intensity of associations between diagnoses and heart failure. For instance, the method showed that established risk factors including myocardial infarction, atrial fibrillation and flutter, and hypertension all strongly associated with the heart failure prediction. Additionally, when population was stratified into different age groups, incident occurrence of a given disease had generally a higher contribution to heart failure prediction in younger ages than when diagnosed later in life. Conclusions Our state-of-the-art deep learning framework outperforms the predictive performance of existing models whilst enabling a data-driven way of exploring the relative contribution of a range of risk factors in the context of other temporal information. Funding Acknowledgement Type of funding source: Private grant(s) and/or Sponsorship. Main funding source(s): National Institute for Health Research, Oxford Martin School, Oxford Biomedical Research Centre

scholarly journals lncRNA_Mdeep: An Alignment-Free Predictor for Distinguishing Long Non-Coding RNAs from Protein-Coding Transcripts by Multimodal Deep Learning

2020 ◽  
Vol 21 (15) ◽  
pp. 5222 ◽  
Author(s):  
Xiao-Nan Fan ◽  
Shao-Wu Zhang ◽  
Song-Yao Zhang ◽  
Jin-Jie Ni
Keyword(s):  
Deep Learning ◽  
Prediction Accuracy ◽  
Protein Coding ◽  
Learning Framework ◽  
Alignment Free ◽  
Independent Test ◽  
Non Coding Rnas ◽  
High Level ◽  
Fold Cross Validation ◽  
Human Complex

Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes and human complex diseases. Distinguishing lncRNAs from protein-coding transcripts is a fundamental step for analyzing the lncRNA functional mechanism. However, the experimental identification of lncRNAs is expensive and time-consuming. In this study, we presented an alignment-free multimodal deep learning framework (namely lncRNA_Mdeep) to distinguish lncRNAs from protein-coding transcripts. LncRNA_Mdeep incorporated three different input modalities, then a multimodal deep learning framework was built for learning the high-level abstract representations and predicting the probability whether a transcript was lncRNA or not. LncRNA_Mdeep achieved 98.73% prediction accuracy in a 10-fold cross-validation test on humans. Compared with other eight state-of-the-art methods, lncRNA_Mdeep showed 93.12% prediction accuracy independent test on humans, which was 0.94%~15.41% higher than that of other eight methods. In addition, the results on 11 cross-species datasets showed that lncRNA_Mdeep was a powerful predictor for predicting lncRNAs.

scholarly journals A Deep Learning Model to predict the Industry Readiness of Engineering Students Community

2021 ◽  
Vol 37 ◽  
pp. 01017
Author(s):  
Ashok Murugesan ◽  
Kumar Ramasamy ◽  
Umadevi Ashok ◽  
Revathy Pandian
Keyword(s):  
Deep Learning ◽  
21St Century ◽  
21St Century Skills ◽  
Engineering Students ◽  
Learning Model ◽  
Skill Assessment ◽  
Technical Knowledge ◽  
Learner Model ◽  
Learning Framework ◽  
Deep Learning Model

Industry readiness of Engineering students community is a big challenge in the recent campus recruitments. 21st century skills are completely mapped with the technical and non – technical knowledge background of the engineering graduates. In this paper the work narrated the process of identifying the parameters for skill assessment of the candidates and derived a learner model using deep learning framework. Further the model can be used to predict the employability readiness of candidates.

scholarly journals lncRNA_Mdeep: an alignment-free predictor for long non-coding RNAs identification by multimodal deep learning

2020 ◽  
Author(s):  
Xiao-Nan Fan ◽  
Shao-Wu Zhang ◽  
Song-Yao Zhang ◽  
Jin-Jie Ni
Keyword(s):  
Deep Learning ◽  
Prediction Accuracy ◽  
Protein Coding ◽  
Learning Framework ◽  
Alignment Free ◽  
Independent Test ◽  
Non Coding Rnas ◽  
High Level ◽  
Fold Cross Validation ◽  
Human Complex

Abstract Background: Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes and human complex diseases. Distinguishing lncRNAs from protein-coding transcripts is a fundamental step for analyzing lncRNA functional mechanism. However, the experimental identification of lncRNAs is expensive and time-consuming. Results: In this study, we present an alignment-free multimodal deep learning framework (namely lncRNA_Mdeep) to distinguish lncRNAs from protein-coding transcripts. LncRNA_Mdeep incorporates three different input modalities (i.e. OFH modality, k-mer modality, and sequence modality), then a multimodal deep learning framework is built for learning the high-level abstract representations and predicting the probability whether a transcript is lncRNA or not. Conclusions: LncRNA_Mdeep achieves 98.73% prediction accuracy in 10-fold cross-validation test on human. Compared with other eight state-of-the-art methods, lncRNA_Mdeep shows 93.12% prediction accuracy independent test on human, which is 0.94%~15.41% higher than that of other eight methods. In addition, the results on 11 cross-species datasets show that lncRNA_Mdeep is a powerful predictor for identifying lncRNAs. The source code can be downloaded from https://github.com/NWPU-903PR/lncRNA_Mdeep.

scholarly journals Image-embodied Knowledge Representation Learning

2017 ◽  
Author(s):  
Ruobing Xie ◽  
Zhiyuan Liu ◽  
Huanbo Luan ◽  
Maosong Sun
Keyword(s):  
Knowledge Representation ◽  
Visual Information ◽  
Representation Learning ◽  
Learning Model ◽  
Experimental Results ◽  
Knowledge Graph ◽  
Embodied Knowledge ◽  
Knowledge Representations ◽  
Conventional Methods ◽  
Image Representations

Entity images could provide significant visual information for knowledge representation learning. Most conventional methods learn knowledge representations merely from structured triples, ignoring rich visual information extracted from entity images. In this paper, we propose a novel Image-embodied Knowledge Representation Learning model (IKRL), where knowledge representations are learned with both triple facts and images. More specifically, we first construct representations for all images of an entity with a neural image encoder. These image representations are then integrated into an aggregated image-based representation via an attention-based method. We evaluate our IKRL models on knowledge graph completion and triple classification. Experimental results demonstrate that our models outperform all baselines on both tasks, which indicates the significance of visual information for knowledge representations and the capability of our models in learning knowledge representations with images.

scholarly journals Seeker: Alignment-free identification of bacteriophage genomes by deep learning

2020 ◽  
Author(s):  
Noam Auslander ◽  
Ayal B. Gussow ◽  
Sean Benler ◽  
Yuri I. Wolf ◽  
Eugene V. Koonin
Keyword(s):  
Deep Learning ◽  
Rapid Detection ◽  
Sequence Similarity ◽  
Biological Entity ◽  
Learning Tool ◽  
Alignment Free ◽  
User Friendly ◽  
Identification And Characterization ◽  
Python Package

SummaryAdvances in metagenomics enable massive discovery of diverse, distinct microbes and viruses. Bacteriophages, the most abundant biological entity on Earth, evolve rapidly, and therefore, detection of unknown bacteriophages in sequence datasets is a challenge. The existing methods rely on sequence similarity to known bacteriophage sequences, impeding the identification and characterization of distinct bacteriophage families. We present Seeker, a deep-learning tool for reference-free identification of phage sequences. Seeker allows rapid detection of phages in sequence datasets and clean differentiation of phage sequences from bacterial ones, even for phages with little sequence similarity to established phage families. We comprehensively validate Seeker’s ability to identify unknown phages and employ Seeker to detect unknown phages, some of which are highly divergent from known phage families. We provide a web portal (seeker.pythonanywhere.com) and a user-friendly python package (https://github.com/gussow/seeker) allowing researchers to easily apply Seeker in metagenomic studies, for the detection of diverse unknown bacteriophages.

scholarly journals Evaluation of Methods for Protein Representation Learning: A Quantitative Analysis

2020 ◽  
Author(s):  
Serbulent Unsal ◽  
Heval Ataş ◽  
Muammer Albayrak ◽  
Kemal Turhan ◽  
Aybar C. Acar ◽  
...  
Keyword(s):  
Deep Learning ◽  
Language Processing ◽  
Complex Traits ◽  
Representation Learning ◽  
Data Representation ◽  
Language Models ◽  
Learning Methods ◽  
Advantages And Disadvantages ◽  
Data Representations ◽  
Novel Methods

AbstractData-centric approaches have been utilized to develop predictive methods for elucidating uncharacterized aspects of proteins such as their functions, biophysical properties, subcellular locations and interactions. However, studies indicate that the performance of these methods should be further improved to effectively solve complex problems in biomedicine and biotechnology. A data representation method can be defined as an algorithm that calculates numerical feature vectors for samples in a dataset, to be later used in quantitative modelling tasks. Data representation learning methods do this by training and using a model that employs statistical and machine/deep learning algorithms. These novel methods mostly take inspiration from the data-driven language models that have yielded ground-breaking improvements in the field of natural language processing. Lately, these learned data representations have been applied to the field of protein informatics and have displayed highly promising results in terms of extracting complex traits of proteins regarding sequence-structure-function relations. In this study, we conducted a detailed investigation over protein representation learning methods, by first categorizing and explaining each approach, and then conducting benchmark analyses on; (i) inferring semantic similarities between proteins, (ii) predicting ontology-based protein functions, and (iii) classifying drug target protein families. We examine the advantages and disadvantages of each representation approach over the benchmark results. Finally, we discuss current challenges and suggest future directions. We believe the conclusions of this study will help researchers in applying machine/deep learning-based representation techniques on protein data for various types of predictive tasks. Furthermore, we hope it will demonstrate the potential of machine learning-based data representations for protein science and inspire the development of novel methods/tools to be utilized in the fields of biomedicine and biotechnology.

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