Deep learning for drug–drug interaction extraction from the literature: a review

AbstractDrug–drug interactions (DDIs) are crucial for drug research and pharmacovigilance. These interactions may cause adverse drug effects that threaten public health and patient safety. Therefore, the DDIs extraction from biomedical literature has been widely studied and emphasized in modern biomedical research. The previous rules-based and machine learning approaches rely on tedious feature engineering, which is labourious, time-consuming and unsatisfactory. With the development of deep learning technologies, this problem is alleviated by learning feature representations automatically. Here, we review the recent deep learning methods that have been applied to the extraction of DDIs from biomedical literature. We describe each method briefly and compare its performance in the DDI corpus systematically. Next, we summarize the advantages and disadvantages of these deep learning models for this task. Furthermore, we discuss some challenges and future perspectives of DDI extraction via deep learning methods. This review aims to serve as a useful guide for interested researchers to further advance bioinformatics algorithms for DDIs extraction from the literature.

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A Review of Computer-Aided Expert Systems for Breast Cancer Diagnosis

Cancers ◽

10.3390/cancers13112764 ◽

2021 ◽

Vol 13 (11) ◽

pp. 2764

Author(s):

Xin Yu Liew ◽

Nazia Hameed ◽

Jeremie Clos

Keyword(s):

Breast Cancer ◽

Machine Learning ◽

Deep Learning ◽

Main Process ◽

Learning Approaches ◽

Learning Methods ◽

Advantages And Disadvantages ◽

Computer Aided ◽

Conventional Methods ◽

The Impact

A computer-aided diagnosis (CAD) expert system is a powerful tool to efficiently assist a pathologist in achieving an early diagnosis of breast cancer. This process identifies the presence of cancer in breast tissue samples and the distinct type of cancer stages. In a standard CAD system, the main process involves image pre-processing, segmentation, feature extraction, feature selection, classification, and performance evaluation. In this review paper, we reviewed the existing state-of-the-art machine learning approaches applied at each stage involving conventional methods and deep learning methods, the comparisons within methods, and we provide technical details with advantages and disadvantages. The aims are to investigate the impact of CAD systems using histopathology images, investigate deep learning methods that outperform conventional methods, and provide a summary for future researchers to analyse and improve the existing techniques used. Lastly, we will discuss the research gaps of existing machine learning approaches for implementation and propose future direction guidelines for upcoming researchers.

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Speech Enhancement Using Deep Learning Methods: A Review

Jurnal Elektronika dan Telekomunikasi ◽

10.14203/jet.v21.19-26 ◽

2021 ◽

Vol 21 (1) ◽

pp. 19

Author(s):

Asri Rizki Yuliani ◽

M. Faizal Amri ◽

Endang Suryawati ◽

Ade Ramdan ◽

Hilman Ferdinandus Pardede

Keyword(s):

Neural Network ◽

Deep Learning ◽

Speech Enhancement ◽

Speech Signal ◽

Research Field ◽

Learning Technologies ◽

Learning Approaches ◽

Speech Signal Processing ◽

Generative Adversarial Network ◽

Advantages And Disadvantages

Speech enhancement, which aims to recover the clean speech of the corrupted signal, plays an important role in the digital speech signal processing. According to the type of degradation and noise in the speech signal, approaches to speech enhancement vary. Thus, the research topic remains challenging in practice, specifically when dealing with highly non-stationary noise and reverberation. Recent advance of deep learning technologies has provided great support for the progress in speech enhancement research field. Deep learning has been known to outperform the statistical model used in the conventional speech enhancement. Hence, it deserves a dedicated survey. In this review, we described the advantages and disadvantages of recent deep learning approaches. We also discussed challenges and trends of this field. From the reviewed works, we concluded that the trend of the deep learning architecture has shifted from the standard deep neural network (DNN) to convolutional neural network (CNN), which can efficiently learn temporal information of speech signal, and generative adversarial network (GAN), that utilize two networks training.

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Comparing Deep Learning and Statistical Methods in Forecasting Crowd Distribution from Aggregated Mobile Phone Data

Applied Sciences ◽

10.3390/app10186580 ◽

2020 ◽

Vol 10 (18) ◽

pp. 6580 ◽

Cited By ~ 1

Author(s):

Alket Cecaj ◽

Marco Lippi ◽

Marco Mamei ◽

Franco Zambonelli

Keyword(s):

Deep Learning ◽

Mobile Phone ◽

Statistical Methods ◽

Urban Areas ◽

Domain Knowledge ◽

Mobile Phone Data ◽

Learning Approaches ◽

Learning Methods ◽

Advantages And Disadvantages ◽

Crowd Density

Accurately forecasting how crowds of people are distributed in urban areas during daily activities is of key importance for the smart city vision and related applications. In this work we forecast the crowd density and distribution in an urban area by analyzing an aggregated mobile phone dataset. By comparing the forecasting performance of statistical and deep learning methods on the aggregated mobile data we show that each class of methods has its advantages and disadvantages depending on the forecasting scenario. However, for our time-series forecasting problem, deep learning methods are preferable when it comes to simplicity and immediacy of use, since they do not require a time-consuming model selection for each different cell. Deep learning approaches are also appropriate when aiming to reduce the maximum forecasting error. Statistical methods instead show their superiority in providing more precise forecasting results, but they require data domain knowledge and computationally expensive techniques in order to select the best parameters.

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Deep Learning Methods for Heart Sounds Classification: A Systematic Review

Entropy ◽

10.3390/e23060667 ◽

2021 ◽

Vol 23 (6) ◽

pp. 667

Author(s):

Wei Chen ◽

Qiang Sun ◽

Xiaomin Chen ◽

Gangcai Xie ◽

Huiqun Wu ◽

...

Keyword(s):

Neural Network ◽

Systematic Review ◽

Deep Learning ◽

Heart Sounds ◽

Learning Approaches ◽

Automated Classification ◽

Learning Methods ◽

Artificial Intelligence Technology ◽

Medical Big Data ◽

Effective Models

The automated classification of heart sounds plays a significant role in the diagnosis of cardiovascular diseases (CVDs). With the recent introduction of medical big data and artificial intelligence technology, there has been an increased focus on the development of deep learning approaches for heart sound classification. However, despite significant achievements in this field, there are still limitations due to insufficient data, inefficient training, and the unavailability of effective models. With the aim of improving the accuracy of heart sounds classification, an in-depth systematic review and an analysis of existing deep learning methods were performed in the present study, with an emphasis on the convolutional neural network (CNN) and recurrent neural network (RNN) methods developed over the last five years. This paper also discusses the challenges and expected future trends in the application of deep learning to heart sounds classification with the objective of providing an essential reference for further study.

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DeepVar: An End-to-End Deep Learning Approach for Genomic Variant Recognition in Biomedical Literature

Proceedings of the AAAI Conference on Artificial Intelligence ◽

10.1609/aaai.v34i01.5399 ◽

2020 ◽

Vol 34 (01) ◽

pp. 598-605

Author(s):

Chaoran Cheng ◽

Fei Tan ◽

Zhi Wei

Keyword(s):

Deep Learning ◽

Large Data ◽

Biomedical Literature ◽

Entity Recognition ◽

Learning Approach ◽

Learning Approaches ◽

Genomic Variants ◽

Low Resource ◽

End To End ◽

Genomic Variant

We consider the problem of Named Entity Recognition (NER) on biomedical scientific literature, and more specifically the genomic variants recognition in this work. Significant success has been achieved for NER on canonical tasks in recent years where large data sets are generally available. However, it remains a challenging problem on many domain-specific areas, especially the domains where only small gold annotations can be obtained. In addition, genomic variant entities exhibit diverse linguistic heterogeneity, differing much from those that have been characterized in existing canonical NER tasks. The state-of-the-art machine learning approaches heavily rely on arduous feature engineering to characterize those unique patterns. In this work, we present the first successful end-to-end deep learning approach to bridge the gap between generic NER algorithms and low-resource applications through genomic variants recognition. Our proposed model can result in promising performance without any hand-crafted features or post-processing rules. Our extensive experiments and results may shed light on other similar low-resource NER applications.

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A general approach for improving deep learning-based medical relation extraction using a pre-trained model and fine-tuning

Database ◽

10.1093/database/baz116 ◽

2019 ◽

Vol 2019 ◽

Cited By ~ 2

Author(s):

Tao Chen ◽

Mingfen Wu ◽

Hexi Li

Keyword(s):

Deep Learning ◽

Large Scale ◽

Relation Extraction ◽

Training Model ◽

Biomedical Literature ◽

Training Data ◽

Fine Tuning ◽

Learning Approaches ◽

Additional Time ◽

Clinical Records

Abstract The automatic extraction of meaningful relations from biomedical literature or clinical records is crucial in various biomedical applications. Most of the current deep learning approaches for medical relation extraction require large-scale training data to prevent overfitting of the training model. We propose using a pre-trained model and a fine-tuning technique to improve these approaches without additional time-consuming human labeling. Firstly, we show the architecture of Bidirectional Encoder Representations from Transformers (BERT), an approach for pre-training a model on large-scale unstructured text. We then combine BERT with a one-dimensional convolutional neural network (1d-CNN) to fine-tune the pre-trained model for relation extraction. Extensive experiments on three datasets, namely the BioCreative V chemical disease relation corpus, traditional Chinese medicine literature corpus and i2b2 2012 temporal relation challenge corpus, show that the proposed approach achieves state-of-the-art results (giving a relative improvement of 22.2, 7.77, and 38.5% in F1 score, respectively, compared with a traditional 1d-CNN classifier). The source code is available at https://github.com/chentao1999/MedicalRelationExtraction.

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Infrared and Visible Image Fusion Techniques Based on Deep Learning: A Review

Electronics ◽

10.3390/electronics9122162 ◽

2020 ◽

Vol 9 (12) ◽

pp. 2162

Author(s):

Changqi Sun ◽

Cong Zhang ◽

Naixue Xiong

Keyword(s):

Deep Learning ◽

Image Fusion ◽

Research Work ◽

Image Features ◽

Future Research ◽

Learning Methods ◽

Visible Image ◽

Advantages And Disadvantages ◽

Fusion Methods ◽

Future Work

Infrared and visible image fusion technologies make full use of different image features obtained by different sensors, retain complementary information of the source images during the fusion process, and use redundant information to improve the credibility of the fusion image. In recent years, many researchers have used deep learning methods (DL) to explore the field of image fusion and found that applying DL has improved the time-consuming efficiency of the model and the fusion effect. However, DL includes many branches, and there is currently no detailed investigation of deep learning methods in image fusion. In this work, this survey reports on the development of image fusion algorithms based on deep learning in recent years. Specifically, this paper first conducts a detailed investigation on the fusion method of infrared and visible images based on deep learning, compares the existing fusion algorithms qualitatively and quantitatively with the existing fusion quality indicators, and discusses various fusions. The main contribution, advantages, and disadvantages of the algorithm. Finally, the research status of infrared and visible image fusion is summarized, and future work has prospected. This research can help us realize many image fusion methods in recent years and lay the foundation for future research work.

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Electric Vehicle Charging Load Forecasting: A Comparative Study of Deep Learning Approaches

Energies ◽

10.3390/en12142692 ◽

2019 ◽

Vol 12 (14) ◽

pp. 2692 ◽

Cited By ~ 12

Author(s):

Juncheng Zhu ◽

Zhile Yang ◽

Monjur Mourshed ◽

Yuanjun Guo ◽

Yimin Zhou ◽

...

Keyword(s):

Deep Learning ◽

Comparative Study ◽

Electric Vehicle ◽

Electric Vehicles ◽

Load Forecasting ◽

Learning Approaches ◽

Short Term ◽

Learning Methods ◽

Electric Vehicle Charging ◽

Vehicle Charging

Load forecasting is one of the major challenges of power system operation and is crucial to the effective scheduling for economic dispatch at multiple time scales. Numerous load forecasting methods have been proposed for household and commercial demand, as well as for loads at various nodes in a power grid. However, compared with conventional loads, the uncoordinated charging of the large penetration of plug-in electric vehicles is different in terms of periodicity and fluctuation, which renders current load forecasting techniques ineffective. Deep learning methods, empowered by unprecedented learning ability from extensive data, provide novel approaches for solving challenging forecasting tasks. This research proposes a comparative study of deep learning approaches to forecast the super-short-term stochastic charging load of plug-in electric vehicles. Several popular and novel deep-learning based methods have been utilized in establishing the forecasting models using minute-level real-world data of a plug-in electric vehicle charging station to compare the forecasting performance. Numerical results of twelve cases on various time steps show that deep learning methods obtain high accuracy in super-short-term plug-in electric load forecasting. Among the various deep learning approaches, the long-short-term memory method performs the best by reducing over 30% forecasting error compared with the conventional artificial neural network model.

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Learning to Combine Local and Global Image Information for Contactless Palmprint Recognition

Sensors ◽

10.3390/s22010073 ◽

2021 ◽

Vol 22 (1) ◽

pp. 73

Author(s):

Marjan Stoimchev ◽

Marija Ivanovska ◽

Vitomir Štruc

Keyword(s):

Deep Learning ◽

State Of The Art ◽

Input Image ◽

Palmprint Recognition ◽

Learning Approaches ◽

Elastic Deformations ◽

Feature Representations ◽

Palmar Surface ◽

Proposed Model ◽

Visual Artifacts

In the past few years, there has been a leap from traditional palmprint recognition methodologies, which use handcrafted features, to deep-learning approaches that are able to automatically learn feature representations from the input data. However, the information that is extracted from such deep-learning models typically corresponds to the global image appearance, where only the most discriminative cues from the input image are considered. This characteristic is especially problematic when data is acquired in unconstrained settings, as in the case of contactless palmprint recognition systems, where visual artifacts caused by elastic deformations of the palmar surface are typically present in spatially local parts of the captured images. In this study we address the problem of elastic deformations by introducing a new approach to contactless palmprint recognition based on a novel CNN model, designed as a two-path architecture, where one path processes the input in a holistic manner, while the second path extracts local information from smaller image patches sampled from the input image. As elastic deformations can be assumed to most significantly affect the global appearance, while having a lesser impact on spatially local image areas, the local processing path addresses the issues related to elastic deformations thereby supplementing the information from the global processing path. The model is trained with a learning objective that combines the Additive Angular Margin (ArcFace) Loss and the well-known center loss. By using the proposed model design, the discriminative power of the learned image representation is significantly enhanced compared to standard holistic models, which, as we show in the experimental section, leads to state-of-the-art performance for contactless palmprint recognition. Our approach is tested on two publicly available contactless palmprint datasets—namely, IITD and CASIA—and is demonstrated to perform favorably against state-of-the-art methods from the literature. The source code for the proposed model is made publicly available.

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Deep Learning for Recommender Systems: A Netflix Case Study

AI Magazine ◽

10.1609/aimag.v42i3.18140 ◽

2022 ◽

Vol 42 (3) ◽

pp. 7-18

Author(s):

Harald Steck ◽

Linas Baltrunas ◽

Ehtsham Elahi ◽

Dawen Liang ◽

Yves Raimond ◽

...

Keyword(s):

Machine Learning ◽

Deep Learning ◽

Recommender Systems ◽

Input Data ◽

Lessons Learned ◽

Learning Approaches ◽

Learning Models ◽

Learning Methods ◽

Recommendation Algorithms

Deep learning has profoundly impacted many areas of machine learning. However, it took a while for its impact to be felt in the field of recommender systems. In this article, we outline some of the challenges encountered and lessons learned in using deep learning for recommender systems at Netflix. We first provide an overview of the various recommendation tasks on the Netflix service. We found that different model architectures excel at different tasks. Even though many deep-learning models can be understood as extensions of existing (simple) recommendation algorithms, we initially did not observe significant improvements in performance over well-tuned non-deep-learning approaches. Only when we added numerous features of heterogeneous types to the input data, deep-learning models did start to shine in our setting. We also observed that deep-learning methods can exacerbate the problem of offline–online metric (mis-)alignment. After addressing these challenges, deep learning has ultimately resulted in large improvements to our recommendations as measured by both offline and online metrics. On the practical side, integrating deep-learning toolboxes in our system has made it faster and easier to implement and experiment with both deep-learning and non-deep-learning approaches for various recommendation tasks. We conclude this article by summarizing our take-aways that may generalize to other applications beyond Netflix.

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