Drug-Drug Interaction Extraction via Recurrent Hybrid Convolutional Neural Networks with an Improved Focal Loss

Application of Artificial Intelligence in Drug-Drug Interactions Prediction: A Review

Drug-drug interactions (DDI) are a critical aspect of drug research that can have adverse effects on patients and can lead to serious consequences. Predicting these events accurately can significantly improve clinicians' ability to make better decisions and establish optimal treatment regimens. However, manually detecting these interactions is time-consuming and labor-intensive. Utilizing the advancements in Artificial Intelligence (AI) is essential for achieving accurate forecasts of DDIs. In this review, DDI prediction tasks are classified into three types according to the type of DDI prediction: undirected DDI prediction, DDI events prediction, and Asymmetric DDI prediction. The paper then reviews the progress of AI for each of these three prediction tasks in DDI and provides a summary of the data sets used as well as the representative methods used in these three prediction directions. In this review, we aim to provide a comprehensive overview of drug interaction prediction. The first section introduces commonly used databases and presents an overview of current research advancements and techniques across three domains of DDI. Additionally, we introduce classical machine learning techniques for predicting undirected drug interactions and provide a timeline for the progression of the predicted drug interaction events. At last, we debate the difficulties and prospects of AI approaches at predicting DDI, emphasizing their potential for improving clinical decision-making and patient outcomes.

SubGE-DDI: A new prediction model for drug-drug interaction established through biomedical texts and drug-pairs knowledge subgraph enhancement

Biomedical texts provide important data for investigating drug-drug interactions (DDIs) in the field of pharmacovigilance. Although researchers have attempted to investigate DDIs from biomedical texts and predict unknown DDIs, the lack of accurate manual annotations significantly hinders the performance of machine learning algorithms. In this study, a new DDI prediction framework, Subgraph Enhance model, was developed for DDI (SubGE-DDI) to improve the performance of machine learning algorithms. This model uses drug pairs knowledge subgraph information to achieve large-scale plain text prediction without many annotations. This model treats DDI prediction as a multi-class classification problem and predicts the specific DDI type for each drug pair (e.g. Mechanism, Effect, Advise, Interact and Negative). The drug pairs knowledge subgraph was derived from a huge drug knowledge graph containing various public datasets, such as DrugBank, TwoSIDES, OffSIDES, DrugCentral, EntrezeGene, SMPDB (The Small Molecule Pathway Database), CTD (The Comparative Toxicogenomics Database) and SIDER. The SubGE-DDI was evaluated from the public dataset (SemEval-2013 Task 9 dataset) and then compared with other state-of-the-art baselines. SubGE-DDI achieves 83.91% micro F1 score and 84.75% macro F1 score in the test dataset, outperforming the other state-of-the-art baselines. These findings show that the proposed drug pairs knowledge subgraph-assisted model can effectively improve the prediction performance of DDIs from biomedical texts.

MTMG: A multi-task model with multi-granularity information for drug-drug interaction extraction

Drug-drug interactions (DDIs) extraction includes identifying drug entities and interactions between drug pairs from the biomedical corpus. The discovery of potential DDIs aids in our understanding of the mechanisms underlying adverse reactions or combination therapy to improve patient safety. The manual extraction of DDIs is very time-consuming and expensive; therefore, computer-aided extraction of DDIs is vital. Many neural network-based methods have been proposed and achieved good efficiency in the extraction of DDIs over the years. However, most studies improved the performance of DDIs extraction with various external drug features while directly using golden drug entities, leading to error propagation and low universality in practical application. In this paper, we propose a new multi-task framework called MTMG, which changes DDIs extraction from a sentence-level classification task to a sequence labeling task named Drug-Specified Token Classification (DSTC). The proposed approach, MTMG, jointly trains DSTC with drug named entity recognition (DNER) and two sentence-level auxiliary tasks we designed. We aim to improve the performance of the entire DDIs extraction pipeline by better using the correlation between entities and relationships and, to the extent possible, using the information of varying granularity implied in the dataset. Experimental results show that MTMG can both improve the accuracy of DNER and DDIs extraction and outperforms state-of-the-art technique.

Biomedical Relation Extraction Using Dependency Graph and Decoder-Enhanced Transformer Model

The identification of drug-drug and chemical-protein interactions is essential for understanding unpredictable changes in the pharmacological effects of drugs and mechanisms of diseases and developing therapeutic drugs. In this study, we extract drug-related interactions from the DDI (Drug-Drug Interaction) Extraction-2013 Shared Task dataset and the BioCreative ChemProt (Chemical-Protein) dataset using various transfer transformers. We propose BERT_GAT that uses a graph attention network (GAT) to take into account the local structure of sentences and embedding features of nodes under the self-attention scheme and investigate whether incorporating syntactic structure can help relation extraction. In addition, we suggest T5_{slim_dec}, which adapts the autoregressive generation task of the T5 (text-to-text transfer transformer) to the relation classification problem by removing the self-attention layer in the decoder block. Furthermore, we evaluated the potential of biomedical relation extraction of GPT-3 (Generative Pre-trained Transformer) using GPT-3 variant models. As a result, T5_{slim_dec}, which is a model with a tailored decoder designed for classification problems within the T5 architecture, demonstrated very promising performances for both tasks. We achieved an accuracy of 91.15% in the DDI dataset and an accuracy of 94.29% for the CPR (Chemical-Protein Relation) class group in ChemProt dataset. However, BERT_GAT did not show a significant performance improvement in the aspect of relation extraction. We demonstrated that transformer-based approaches focused only on relationships between words are implicitly eligible to understand language well without additional knowledge such as structural information.

MSEDDI: Multi-Scale Embedding for Predicting Drug-Drug Interaction Events

A norm in modern medicine is to prescribe polypharmacy to treat disease. The core concern with the co-administration of drugs is that it may produce adverse drug-drug interaction (DDI), which can cause unexpected bodily injury. Therefore, it is essential to identify potential DDI. Most existing methods in silico only judge whether two drugs interact, ignoring the importance of interaction events to study the mechanism implied in combination drugs. In this work, we propose a deep learning framework named MSEDDI that comprehensively considers multi-scale embedding representations of the drug for predicting drug-drug interaction events. In MSEDDI, we design three-channel networks to process biomedical network-based knowledge graph embedding, SMILES sequence-based notation embedding, and molecular graph-based chemical structure embedding, respectively. Finally, we fuse three heterogeneous features from channel outputs through a self-attention mechanism and feed them to the linear layer predictor. In the experimental section, we evaluate the performance of all methods on two different prediction tasks on two datasets. The results show that MSEDDI outperforms other state-of-the-art baselines. Moreover, we also reveal the stable performance of our model in a broader sample set via case studies.

EMSI-BERT: Asymmetrical Entity-Mask Strategy and Symbol-Insert Structure for Drug–Drug Interaction Extraction Based on BERT

Drug-drug interaction (DDI) extraction has seen growing usage of deep models, but their effectiveness has been restrained by limited domain-labeled data, a weak representation of co-occurring entities, and poor adaptation of downstream tasks. This paper proposes a novel EMSI-BERT method for drug–drug interaction extraction based on an asymmetrical Entity-Mask strategy and a Symbol-Insert structure. Firstly, the EMSI-BERT method utilizes the asymmetrical Entity-Mask strategy to address the weak representation of co-occurring entity information using the drug entity dictionary in the pre-training BERT task. Secondly, the EMSI-BERT method incorporates four symbols to distinguish different entity combinations of the same input sequence and utilizes the Symbol-Insert structure to address the week adaptation of downstream tasks in the fine-tuning stage of DDI classification. The experimental results showed that EMSI-BERT for DDI extraction achieved a 0.82 F1-score on DDI-Extraction 2013, and it improved the performances of the multi-classification task of DDI extraction and the two-classification task of DDI detection. Compared with baseline Basic-BERT, the proposed pre-training BERT with the asymmetrical Entity-Mask strategy could obtain better effects in downstream tasks and effectively limit “Other” samples’ effects. The model visualization results illustrated that EMSI-BERT could extract semantic information at different levels and granularities in a continuous space.

DDI-MuG: Multi-aspect graphs for drug-drug interaction extraction

Introduction

Drug-drug interaction (DDI) may lead to adverse reactions in patients, thus it is important to extract such knowledge from biomedical texts. However, previously proposed approaches typically focus on capturing sentence-aspect information while ignoring valuable knowledge concerning the whole corpus. In this paper, we propose a Multi-aspect Graph-based DDI extraction model, named DDI-MuG.

Methods

We first employ a bio-specific pre-trained language model to obtain the token contextualized representations. Then we use two graphs to get syntactic information from input instance and word co-occurrence information within the entire corpus, respectively. Finally, we combine the representations of drug entities and verb tokens for the final classification.

Results

To validate the effectiveness of the proposed model, we perform extensive experiments on two widely used DDI extraction dataset, DDIExtraction-2013 and TAC 2018. It is encouraging to see that our model outperforms all twelve state-of-the-art models.

Discussion

In contrast to the majority of earlier models that rely on the black-box approach, our model enables visualization of crucial words and their interrelationships by utilizing edge information from two graphs. To the best of our knowledge, this is the first model that explores multi-aspect graphs to the DDI extraction task, and we hope it can establish a foundation for more robust multi-aspect works in the future.

Artificial intelligence-driven prediction of multiple drug interactions

When a drug is administered to exert its efficacy, it will encounter multiple barriers and go through multiple interactions. Predicting the drug-related multiple interactions is critical for drug development and safety monitoring because it provides foundations for practical, safe compatibility and rational use of multiple drugs. With the progress of artificial intelligence (AI) technology, a variety of novel prediction methods for single interaction have emerged and shown great advantages compared to the traditional, expensive and time-consuming laboratory research. To promote the comprehensive and simultaneous predictions of multiple interactions, we systematically reviewed the application of AI in drug-drug, drug-food (excipients) and drug-microbiome interactions. We began by outlining the model methods, evaluation indicators, algorithms and databases commonly used to build models for three types of drug interactions. The models based on the metabolic enzyme P450, drug similarity and drug targets have empathized among the machine learning models of drug-drug interactions. In particular, we discussed the limitations of current approaches and identified potential areas for future research. It is anticipated the in-depth review will be helpful for the development of the next-generation of systematic prediction models for simultaneous multiple interactions.

IMLBoost for intelligent diagnosis with imbalanced medical records

Class imbalance of medical records is a critical challenge for disease classification in intelligent diagnosis. Existing machine learning algorithms usually assign equal weights to all classes, which may reduce classification accuracy of imbalanced records. In this paper, a new Imbalance Lessened Boosting (IMLBoost) algorithm is proposed to better classify imbalanced medical records, highlighting the contribution of samples in minor classes as well as hard and boundary samples. A tailored Cost-Fitting Loss (CFL) function is proposed to assign befitting costs to these critical samples. The first and second derivations of the CFL are then derived and embedded into the classical XGBoost framework. In addition, some feature analysis skills are utilized to further improve performance of the IMLBoost, which also can speed up the model training. Experimental results on five UCI imbalanced medical datasets have demonstrated the effectiveness of the proposed algorithm. Compared with other existing classification methods, IMLBoost has improved the classification performance in terms of F1-score, G-mean and AUC.

Extracting drug-drug interactions from no-blinding texts using key semantic sentences and GHM loss

The extraction of drug-drug interactions (DDIs) is an important task in the field of biomedical research, which can reduce unexpected health risks during patient treatment. Previous work indicates that methods using external drug information have a much higher performance than those methods not using it. However, the use of external drug information is time-consuming and resource-costly. In this work, we propose a novel method for extracting DDIs which does not use external drug information, but still achieves comparable performance. First, we no longer convert the drug name to standard tokens such as DRUG0, the method commonly used in previous research. Instead, full drug names with drug entity marking are input to BioBERT, allowing us to enhance the selected drug entity pair. Second, we adopt the Key Semantic Sentence approach to emphasize the words closely related to the DDI relation of the selected drug pair. After the above steps, the misclassification of similar instances which are created from the same sentence but corresponding to different pairs of drug entities can be significantly reduced. Then, we employ the Gradient Harmonizing Mechanism (GHM) loss to reduce the weight of mislabeled instances and easy-to-classify instances, both of which can lead to poor performance in DDI extraction. Overall, we demonstrate in this work that it is better not to use drug blinding with BioBERT, and show that GHM performs better than Cross-Entropy loss if the proportion of label noise is less than 30%. The proposed model achieves state-of-the-art results with an F1-score of 84.13% on the DDIExtraction 2013 corpus (a standard English DDI corpus), which fills the performance gap (4%) between methods that rely on and do not rely on external drug information.

A Comprehensive Review of Computational Methods For Drug-Drug Interaction Detection

The detection of drug-drug interactions (DDIs) is a crucial task for drug safety surveillance, which provides effective and safe co-prescriptions of multiple drugs. Since laboratory researches are often complicated, costly and time-consuming, it's urgent to develop computational approaches to detect drug-drug interactions. In this paper, we conduct a comprehensive review of state-of-the-art computational methods falling into three categories: literature-based extraction methods, machine learning-based prediction methods and pharmacovigilance-based data mining methods. Literature-based extraction methods detect DDIs from published literature using natural language processing techniques; machine learning-based prediction methods build prediction models based on the known DDIs in databases and predict novel ones; pharmacovigilance-based data mining methods usually apply statistical techniques on various electronic data to detect drug-drug interaction signals. We first present the taxonomy of drug-drug interaction detection methods and provide the outlines of three categories of methods. Afterwards, we respectively introduce research backgrounds and data sources of three categories, and illustrate their representative approaches as well as evaluation metrics. Finally, we discuss the current challenges of existing methods and highlight potential opportunities for future directions.

Research on Feature Extraction and Chinese Translation Method of Internet-of-Things English Terminology

Feature extraction and Chinese translation of Internet-of-Things English terms are the basis of many natural language processing. Its main purpose is to extract rich semantic information from unstructured texts to allow computers to further calculate and process them to meet different types of NLP-based tasks. However, most of the current methods use simple neural network models to count the word frequency or probability of words in the text, and it is difficult to accurately understand and translate IoT English terms. In response to this problem, this study proposes a neural network for feature extraction and Chinese translation of IoT English terms based on LSTM, which can not only correctly extract and translate IoT English vocabulary but also realize the feature correspondence between English and Chinese. The neural network proposed in this study has been tested and trained on multiple datasets, and it basically fulfills the requirements of feature translation and Chinese translation of Internet-of-Things terms in English and has great potential in the follow-up work.

Drug-Drug Interactions Prediction Using Fingerprint Only

Combination drug therapy is an efficient way to treat complicated diseases. Drug-drug interaction (DDI) is an important research topic in this therapy as patient safety is a problem when two or more drugs are taken at the same time. Traditionally, in vitro experiments and clinical trials are common ways to determine DDIs. However, these methods cannot meet the requirements of large-scale tests. It is an alternative way to develop computational methods for predicting DDIs. Although several previous methods have been proposed, they always need several types of drug information, limiting their applications. In this study, we proposed a simple computational method to predict DDIs. In this method, drugs were represented by their fingerprint features, which are most widely used in investigating drug-related problems. These features were refined by three models, including addition, subtraction, and Hadamard models, to generate the representation of DDIs. The powerful classification algorithm, random forest, was picked up to build the classifier. The results of two types of tenfold cross-validation on the classifier indicated good performance for discovering novel DDIs among known drugs and acceptable performance for identifying DDIs between known drugs and unknown drugs or among unknown drugs. Although the classifier adopted a sample scheme to represent DDIs, it was still superior to other methods, which adopted features generated by some advanced computer algorithms. Furthermore, a user-friendly web-server, named DDIPF (http://106.14.164.77:5004/DDIPF/), was developed to implement the classifier.

On the road to explainable AI in drug-drug interactions prediction: a systematic review

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A systematic review on applications of explainable AI in drug-drug interaction prediction.

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Review is conducted on a comprehensive set of 94 papers from five prestigious databases.

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Discussions on the promises and challenges of explainable AI algorithms for drug-drug interaction prediction.

Over the past decade, polypharmacy instances have been common in multi-diseases treatment. However, unwanted drug-drug interactions (DDIs) that might cause unexpected adverse drug events (ADEs) in multiple regimens therapy remain a significant issue. Since artificial intelligence (AI) is ubiquitous today, many AI prediction models have been developed to predict DDIs to support clinicians in pharmacotherapy-related decisions. However, even though DDI prediction models have great potential for assisting physicians in polypharmacy decisions, there are still concerns regarding the reliability of AI models due to their black-box nature. Building AI models with explainable mechanisms can augment their transparency to address the above issue. Explainable AI (XAI) promotes safety and clarity by showing how decisions are made in AI models, especially in critical tasks like DDI predictions. In this review, a comprehensive overview of AI-based DDI prediction, including the publicly available source for AI-DDIs studies, the methods used in data manipulation and feature preprocessing, the XAI mechanisms to promote trust of AI, especially for critical tasks as DDIs prediction, the modeling methods, is provided. Limitations and the future directions of XAI in DDIs are also discussed.

Big Data Management in Drug–Drug Interaction: A Modern Deep Learning Approach for Smart Healthcare

The detection and classification of drug–drug interactions (DDI) from existing data are of high importance because recent reports show that DDIs are among the major causes of hospital-acquired conditions and readmissions and are also necessary for smart healthcare. Therefore, to avoid adverse drug interactions, it is necessary to have an up-to-date knowledge of DDIs. This knowledge could be extracted by applying text-processing techniques to the medical literature published in the form of ‘Big Data’ because, whenever a drug interaction is investigated, it is typically reported and published in healthcare and clinical pharmacology journals. However, it is crucial to automate the extraction of the interactions taking place between drugs because the medical literature is being published in immense volumes, and it is impossible for healthcare professionals to read and collect all of the investigated DDI reports from these Big Data. To avoid this time-consuming procedure, the Information Extraction (IE) and Relationship Extraction (RE) techniques that have been studied in depth in Natural Language Processing (NLP) could be very promising. Since 2011, a lot of research has been reported in this particular area, and there are many approaches that have been implemented that can also be applied to biomedical texts to extract DDI-related information. A benchmark corpus is also publicly available for the advancement of DDI extraction tasks. The current state-of-the-art implementations for extracting DDIs from biomedical texts has employed Support Vector Machines (SVM) or other machine learning methods that work on manually defined features and that might be the cause of the low precision and recall that have been achieved in this domain so far. Modern deep learning techniques have also been applied for the automatic extraction of DDIs from the scientific literature and have proven to be very promising for the advancement of DDI extraction tasks. As such, it is pertinent to investigate deep learning techniques for the extraction and classification of DDIs in order for them to be used in the smart healthcare domain. We proposed a deep neural network-based method (SEV-DDI: Severity-Drug–Drug Interaction) with some further-integrated units/layers to achieve higher precision and accuracy. After successfully outperforming other methods in the DDI classification task, we moved a step further and utilized the methods in a sentiment analysis task to investigate the severity of an interaction. The ability to determine the severity of a DDI will be very helpful for clinical decision support systems in making more accurate and informed decisions, ensuring the safety of the patients.

DREAM: Drug-Drug Interaction Extraction with Enhanced Dependency Graph and Attention Mechanism

Drug-drug interactions (DDIs) aim at describing the effect relations produced by a combination of two or more drugs. It is an important semantic processing task in the field of bioinformatics such as pharmacovigilance and clinical research. Recently, graph neural networks are applied on dependency graph to promote the performance of DDI extraction with better semantic representations. However, current method concentrates more on first-order dependency relations and cannot discriminate the connected nodes properly. To better incorporate the dependency relations and improve the representations, we propose a novel DDI extraction method named Drug-drug Interactions extRaction with Enhanced Dependency Graph and Attention Mechanism in this work. Specifically, the dependency graph is enhanced with some potential long-range words to complete the semantic information and fit the aggregation process of graph neural networks. And graph attention mechanism is adopted to further improve word representation by discriminating the connected nodes according to the specific task. Numerical experiments on DDIExtraction 2013 corpus, the benchmark corpus for this domain, demonstrate the superiority of our proposed method.

An annotated corpus from biomedical articles to construct a drug-food interaction database

MOTIVATION

While drug-food interaction (DFI) may undermine the efficacy and safety of drugs, DFI detection has been difficult because a well-organized database for DFI did not exist. To construct a DFI database and build a natural language processing system extracting DFI from biomedical articles, we formulated the DFI extraction tasks and manually annotated texts that could have contained DFI information. In this article, we introduced a new annotated corpus for extracting DFI, the DFI corpus.

RESULTS

The DFI corpus contains 2270 abstracts of biomedical articles accessible through PubMed and 2498 sentences that contain DFI and/or drug-drug information (DDI), a substantial amount of information about drug/food entities, evidence-levels of abstracts and relations between named entities. BERT models pre-trained on the biomedical domain achieved a F1 score 55.0% in extracting DFI key-sentences. To the best of our knowledge, the DFI corpus is the largest public corpus for drug-food interaction.

AVAILABILITY AND IMPLEMENTATION

Our corpus is available at https://github.com/ccadd-snu/corpus-for-DFI-extraction.

Convolutional neural networks (CNNs): concepts and applications in pharmacogenomics

Convolutional neural networks (CNNs) have been used to extract information from various datasets of different dimensions. This approach has led to accurate interpretations in several subfields of biological research, like pharmacogenomics, addressing issues previously faced by other computational methods. With the rising attention for personalized and precision medicine, scientists and clinicians have now turned to artificial intelligence systems to provide them with solutions for therapeutics development. CNNs have already provided valuable insights into biological data transformation. Due to the rise of interest in precision and personalized medicine, in this review, we have provided a brief overview of the possibilities of implementing CNNs as an effective tool for analyzing one-dimensional biological data, such as nucleotide and protein sequences, as well as small molecular data, e.g., simplified molecular-input line-entry specification, InChI, binary fingerprints, etc., to categorize the models based on their objective and also highlight various challenges. The review is organized into specific research domains that participate in pharmacogenomics for a more comprehensive understanding. Furthermore, the future intentions of deep learning are outlined.

Attention-Gated Graph Convolutions for Extracting Drug Interaction Information from Drug Labels

Preventable adverse events as a result of medical errors present a growing concern in the healthcare system. As drug-drug interactions (DDIs) may lead to preventable adverse events, being able to extract DDIs from drug labels into a machine-processable form is an important step toward effective dissemination of drug safety information. Herein, we tackle the problem of jointly extracting mentions of drugs and their interactions, including interaction outcome, from drug labels. Our deep learning approach entails composing various intermediate representations, including graph-based context derived using graph convolutions (GCs) with a novel attention-based gating mechanism (holistically called GCA), which are combined in meaningful ways to predict on all subtasks jointly. Our model is trained and evaluated on the 2018 TAC DDI corpus. Our GCA model in conjunction with transfer learning performs at 39.20% F1 and 26.09% F1 on entity recognition (ER) and relation extraction (RE), respectively, on the first official test set and at 45.30% F1 and 27.87% F1 on ER and RE, respectively, on the second official test set. These updated results lead to improvements over our prior best by up to 6 absolute F1 points. After controlling for available training data, the proposed model exhibits state-of-the-art performance for this task.

Drug-Drug interaction extraction using a position and similarity fusion-based attention mechanism

Taking multiple drugs at the same time can increase or decrease each drug's effectiveness or cause side effects. These drug-drug interactions (DDIs) may lead to an increase in the cost of medical care or even threaten patients' health and life. Thus, automatic extraction of DDIs is an important research field to improve patient safety. In this work, a deep neural network model is presented for extracting DDIs from medical texts. This model utilizes a novel attention mechanism for improving the discrimination of important words from others, based on the word similarities and their relative position with respect to candidate drugs. This approach is applied for calculating the attention weights for the outputs of a bi-directional long short-term memory (Bi-LSTM) model in the deep network structure before detecting the type of DDIs. The proposed method was tested on the standard DDI Extraction 2013 dataset and according to experimental results was able to achieve an F1-Score of 78.30 which is comparable to the best results reported for the state-of-the-art methods. A detailed study of the proposed method and its components is also provided.

Text Semantic Classification of Long Discourses Based on Neural Networks with Improved Focal Loss

Semantic classification of Chinese long discourses is an important and challenging task. Discourse text is high-dimensional and sparse. Furthermore, when the number of classes of dataset is large, the data distribution will be seriously imbalanced. In solving these problems, we propose a novel end-to-end model called CRAFL, which is based on the convolutional layer with attention mechanism, recurrent neural networks, and improved focal loss function. First, the residual network (ResNet) extracts phrase semantic representations from word embedding vectors and reduces the dimensionality of the input matrix. Then, the attention mechanism differentiates the focus on the output of ResNet, and the long short-term memory layer learns the features of the sequences. Lastly but most significantly, we apply an improved focal loss function to mitigate the problem of data class imbalance. Our model is compared with other state-of-the-art models on the long discourse dataset, and CRAFL model has proven be more efficient for this task.

Identifying side effects of commonly used drugs in the treatment of Covid 19

To increase the success in Covid 19 treatment, many drug suggestions are presented, and some clinical studies are shared in the literature. There have been some attempts to use some of these drugs in combination. However, using more than one drug together may cause serious side effects on patients. Therefore, detecting drug-drug interactions of the drugs used will be of great importance in the treatment of Covid 19. In this study, the interactions of 8 drugs used for Covid 19 treatment with 645 different drugs and possible side effects estimates have been produced using Graph Convolutional Networks. As a result of the experiments, it has been found that the hematopoietic system and the cardiovascular system are exposed to more side effects than other organs. Among the focused drugs, Heparin and Atazanavir appear to cause more adverse reactions than other drugs. In addition, as it is known that some of these 8 drugs are used together in Covid-19 treatment, the side effects caused by using these drugs together are shared. With the experimental results obtained, it is aimed to facilitate the selection of the drugs and increase the success of Covid 19 treatment according to the targeted patient.

Medical Information Extraction in the Age of Deep Learning

OBJECTIVES

We survey recent developments in medical Information Extraction (IE) as reported in the literature from the past three years. Our focus is on the fundamental methodological paradigm shift from standard Machine Learning (ML) techniques to Deep Neural Networks (DNNs). We describe applications of this new paradigm concentrating on two basic IE tasks, named entity recognition and relation extraction, for two selected semantic classes-diseases and drugs (or medications)-and relations between them.

METHODS

For the time period from 2017 to early 2020, we searched for relevant publications from three major scientific communities: medicine and medical informatics, natural language processing, as well as neural networks and artificial intelligence.

RESULTS

In the past decade, the field of Natural Language Processing (NLP) has undergone a profound methodological shift from symbolic to distributed representations based on the paradigm of Deep Learning (DL). Meanwhile, this trend is, although with some delay, also reflected in the medical NLP community. In the reporting period, overwhelming experimental evidence has been gathered, as illustrated in this survey for medical IE, that DL-based approaches outperform non-DL ones by often large margins. Still, small-sized and access-limited corpora create intrinsic problems for data-greedy DL as do special linguistic phenomena of medical sublanguages that have to be overcome by adaptive learning strategies.

CONCLUSIONS

The paradigm shift from (feature-engineered) ML to DNNs changes the fundamental methodological rules of the game for medical NLP. This change is by no means restricted to medical IE but should also deeply influence other areas of medical informatics, either NLP- or non-NLP-based.

Extracting drug-drug interactions from texts with BioBERT and multiple entity-aware attentions

Drug-drug interactions (DDIs) extraction is one of the important tasks in the field of biomedical relation extraction, which plays an important role in the field of pharmacovigilance. Previous neural network based models have achieved good performance in DDIs extraction. However, most of the previous models did not make good use of the information of drug entity names, which can help to judge the relation between drugs. This is mainly because drug names are often very complex, leading to the fact that neural network models cannot understand their semantics directly. To address this issue, we propose a DDIs extraction model using multiple entity-aware attentions with various entity information. We use an output-modified bidirectional transformer (BioBERT) and a bidirectional gated recurrent unit layer (BiGRU) to obtain the vector representation of sentences. The vectors of drug description documents encoded by Doc2Vec are used as drug description information, which is an external knowledge to our model. Then we construct three different kinds of entity-aware attentions to get the sentence representations with entity information weighted, including attentions using the drug description information. The outputs of attention layers are concatenated and fed into a multi-layer perception layer. Finally, we get the result by a softmax classifier. The F-score is used to evaluate our model, which is also adopted by most previous DDIs extraction models. We evaluate our proposed model on the DDIExtraction 2013 corpus, which is the benchmark corpus of this domain, and achieves the state-of-the-art result (80.9% in F-score).

Convolutional Recurrent Neural Networks with a Self-Attention Mechanism for Personnel Performance Prediction

Personnel performance is important for the high-technology industry to ensure its core competitive advantages are present. Therefore, predicting personnel performance is an important research area in human resource management (HRM). In this paper, to improve prediction performance, we propose a novel framework for personnel performance prediction to help decision-makers to forecast future personnel performance and recruit the best suitable talents. Firstly, a hybrid convolutional recurrent neural network (CRNN) model based on self-attention mechanism is presented, which can automatically learn discriminative features and capture global contextual information from personnel performance data. Moreover, we treat the prediction problem as a classification task. Then, the k-nearest neighbor (KNN) classifier was used to predict personnel performance. The proposed framework is applied to a real case of personnel performance prediction. The experimental results demonstrate that the presented approach achieves significant performance improvement for personnel performance compared to existing methods.