Drug Disease Relation Extraction from Biomedical Literature Using NLP and Machine Learning

Purpose Improving healthcare services by developing assistive technologies includes both the health aid devices and the analysis of the data collected by them. The acquired data modeled as a knowledge base give more insight into each patient’s health status and needs. Therefore, the ultimate goal of a health-care system is obtaining recommendations provided by an assistive decision support system using such knowledge base, benefiting the patients, the physicians and the healthcare industry. This paper aims to define the knowledge flow for a medical assistive decision support system by structuring raw medical data and leveraging the knowledge contained in the data proposing solutions for efficient data search, medical investigation or diagnosis and medication prediction and relationship identification. Design/methodology/approach The solution this paper proposes for implementing a medical assistive decision support system can analyze any type of unstructured medical documents which are processed by applying Natural Language Processing (NLP) tasks followed by semantic analysis, leading to the medical concept identification, thus imposing a structure on the input documents. The structured information is filtered and classified such that custom decisions regarding patients’ health status can be made. The current research focuses on identifying the relationships between medical concepts as defined by the REMed (Relation Extraction from Medical documents) solution that aims at finding the patterns that lead to the classification of concept pairs into concept-to-concept relations. Findings This paper proposed the REMed solution expressed as a multi-class classification problem tackled using the support vector machine classifier. Experimentally, this paper determined the most appropriate setup for the multi-class classification problem which is a combination of lexical, context, syntactic and grammatical features, as each feature category is good at representing particular relations, but not all. The best results we obtained are expressed as F1-measure of 74.9 per cent which is 1.4 per cent better than the results reported by similar systems. Research limitations/implications The difficulty to discriminate between TrIP and TrAP relations revolves around the hierarchical relationship between the two classes as TrIP is a particular type (an instance) of TrAP. The intuition behind this behavior was that the classifier cannot discern the correct relations because of the bias toward the majority classes. The analysis was conducted by using only sentences from electronic health record that contain at least two medical concepts. This limitation was introduced by the availability of the annotated data with reported results, as relations were defined at sentence level. Originality/value The originality of the proposed solution lies in the methodology to extract valuable information from the medical records via semantic searches; concept-to-concept relation identification; and recommendations for diagnosis, treatment and further investigations. The REMed solution introduces a learning-based approach for the automatic discovery of relations between medical concepts. We propose an original list of features: lexical – 3, context – 6, grammatical – 4 and syntactic – 4. The similarity feature introduced in this paper has a significant influence on the classification, and, to the best of the authors’ knowledge, it has not been used as feature in similar solutions.

Abstract:Bankruptcy prediction and credit scoring are the two important problems facing financial decision support. The multilayer perceptron (MLP) network has shown its applicability to these problems and its performance is usually superior to those of other traditional statistical models. Support vector machines (SVMs) are the core machine learning techniques and have been used to compare with MLP as the benchmark. However, the performance of SVMs is not fully understood in the literature because an insufficient number of data sets is considered and different kernel functions are used to train the SVMs. In this paper, four public data sets are used. In particular, three different sizes of training and testing data in each of the four data sets are considered (i.e. 3:7, 1:1 and 7:3) in order to examine and fully understand the performance of SVMs. For SVM model construction, the linear, radial basis function and polynomial kernel functions are used to construct the SVMs. Using MLP as the benchmark, the SVM classifier only performs better in one of the four data sets. On the other hand, the prediction results of the MLP and SVM classifiers are not significantly different for the three different sizes of training and testing data.

The problem with development of the support vector machine (SVM) classifiers using modified particle swarm optimization (PSO) algorithm and their ensembles has been considered. Solving this problem would allow fulfilling the high-precision data classification, especially Big Data classification, with the acceptable time expenditures. The modified PSO algorithm conducts a simultaneous search of the type of kernel functions, the parameters of the kernel function and the value of the regularization parameter for the SVM classifier. The idea of particles' «regeneration» served as the basis for the modified PSO algorithm. In the implementation of this algorithm, some particles change the type of their kernel function to the one which corresponds to the particle with the best value of the classification accuracy. The offered PSO algorithm allows reducing the time expenditures for the developed SVM classifiers, which is very important for Big Data classification problem. In most cases such SVM classifier provides the high quality of data classification. In exceptional cases the SVM ensembles based on the decorrelation maximization algorithm for the different strategies of the decision-making on the data classification and the majority vote rule can be used. Also, the two-level SVM classifier has been offered. This classifier works as the group of the SVM classifiers at the first level and as the SVM classifier on the base of the modified PSO algorithm at the second level. The results of experimental studies confirm the efficiency of the offered approaches for Big Data classification.

The aim of this study is to extract impervious surfaces and show their spatial distribution, using different machine learning algorithms. For this purpose, geoprocessing and remote sensing techniques were used and three classification methods for digital images were compared, namely Support Vector Machines (SVM), Maximum Likelihood (ML) and Random Trees (RT) classifiers. The study area is one of the most prestigious and the largest housing estates in Warsaw (Poland), the Fort Bema housing complex, which is also an exemplary model for hydrological solutions. The study was prepared on the Geographic Information System platform (GIS) using aerial optical images, orthorectified and thus provided with a suitable coordinate system. The use of these data is therefore supported by the accuracy of the resulting infrared channel product with a pixel size of 0.25 m, making the results much more accurate compared to satellite imagery. The results of the SVM, ML and RT classifiers were compared using the confusion matrix, accuracy (Root Mean Square Error /RMSE/) and kappa index. This showed that the three algorithms were able to successfully discriminate between targets. Overall, the three classifiers had errors, but specifically for impervious surfaces, the highest accuracy was achieved with the SVM classifier (the highest percentage of overall accuracy), followed by ML and RT with 91.51%, 91.35% and 84.52% of the results, respectively. A comparison of the visual results and the confusion matrix shows that although visually the RT method appears to be the most detailed classification into pervious and impervious surfaces, the results were not always correct, e.g., water/shadow was detected as an impervious surface. The NDVI index was also mapped for the same spatial study area and its application in the evaluation of pervious surfaces was explained. The results obtained with the GIS platform, presented in this paper, provide a better understanding of how these advanced classifiers work, which in turn can provide insightful guidance for their selection and combination in real-world applications. The paper also provides an overview of the main works/studies dealing with impervious surface mapping, with different methods for their assessment (including the use of conventional remote sensing, NDVI, multisensory and cross-source data, ‘social sensing’ and classification methods such as SVM, ML and RT), as well as an overview of the research results.

Recognizing textual entailment comprises the task of determining semantic entailment relations between text fragments. A text fragment entails another text fragment if, from the meaning of the former, one can infer the meaning of the latter. If such relation is bidirectional, then we are in the presence of a paraphrase. Automatically recognizing textual entailment relations captures major semantic inference needs in several natural language processing (NLP) applications. As in many NLP tasks, textual entailment corpora for English abound, while the same is not true for more resource-scarce languages such as Portuguese. Exploiting what seems to be the only Portuguese corpus for textual entailment and paraphrases (the ASSIN corpus), in this paper, we address the task of automatically recognizing textual entailment (RTE) and paraphrases from text written in the Portuguese language, by employing supervised machine learning techniques. We employ lexical, syntactic and semantic features, and analyze the impact of using semantic-based approaches in the performance of the system. We then try to take advantage of the bi-dialect nature of ASSIN to compensate its limited size. With the same aim, we explore modeling the task of recognizing textual entailment and paraphrases as a binary classification problem by considering the bidirectional nature of paraphrases as entailment relationships. Addressing the task as a multi-class classification problem, we achieve results in line with the winner of the ASSIN Challenge. In addition, we conclude that semantic-based approaches are promising in this task, and that combining data from European and Brazilian Portuguese is less straightforward than it may initially seem. The binary classification modeling of the problem does not seem to bring advantages to the original multi-class model, despite the outstanding results obtained by the binary classifier for recognizing textual entailments.

In order to improve the performance of Support Vector Machine (SVM) classifier for imbalanced data, this paper proposes dynamic cost-sensitive SVM classifier based on chaos particle swarm optimization (CPDC_SVM). Firstly, this paper introduces dynamic cost-sensitive thought to SVM classifier, and gives the method for structuring dynamic cost and cost-sensitive SVM model. Secondly, we propose the evaluation methodology performance for classifier, and adopts decimal base to code the particles. At last, chaos thought is introduced in particle swarm optimization algorithm, and the Algorithm of the dynamic cost-sensitive SVM classifier is given, which improves convergent speed and accuracy of particle swarm optimization, and can optimize dynamic cost-sensitive SVM well, so CPDC_SVM adds effectively the convergence speed and accuracy for the particle swarm optimization algorithm. Experimental results show CPDC_SVM has higher precision than traditional SVM classifier, and dynamic cost and chaos particle swarm optimization can improve the performance for classifier.

Optical image provides a unique spectral and textural opportunity to acquire data free of charge in cloud-free weather conditions. However, textural information from recent Sentinel-2A data has not been sufficiently recognized. Several researches have shown that texture features are essential for extracting crop information. This study presents a new scheme that integrates spectral bands and textural features for mapping maize fields and other land cover types (i.e., build-up, trees, others, and water) and evaluates the effectiveness of random forest (RF) and support vector machine (SVM) classifiers with different kernel functions based on Sentinel 2A (S-2A) data. The textural features were derived from multiple bands of S-2A image using a grey-level co-occurrence matrix (GLCM) algorithm. To normalize the analysis of these features, Random Forest feature selection was employed. The outcomes show that S-2A images are appropriate for mapping maize fields and other land covers when the image is accessible during the growing season. The SVM classifier with a radial basis function (RBF) kernel is superior to a polynomial (P), linear (L), and sigmoid (S) kernel functions, and the RF classifiers. For the SVM_RBF, the highest overall accuracy was obtained from the integration of spectral bands and textural features at scenario 2 SVM_RBF (87.40%), followed by the combination of spectral and textural features at scenario 2 SVM_P kernel (86.56%). However, scenario 5 SVM_P kernel (85.54%), scenario 4 SVM_P kernel function (85.30%), the spectral features alone, and the SVM_P kernel function, have the highest O/A (83.90%) than that of the SVM_RBF (83.66%). The inclusion of textural features contributed significantly in mapping the smallholder’s maize field in the study area. This demonstrated the value of S-2A in agricultural research.

Researchers analyze data, information, and knowledge through many sources, formats, and methods. The dominant data format includes text and images. In the healthcare industry, professionals generate a large quantity of unstructured data. The complexity of this data and the lack of computational power causes delays in analysis. However, with emerging deep learning algorithms and access to computational powers such as graphics processing unit (GPU) and tensor processing units (TPUs), processing text and images is becoming more accessible. Deep learning algorithms achieve remarkable results in natural language processing (NLP) and computer vision. In this study, we focus on NLP in the healthcare industry and collect data not only from electronic medical records (EMRs) but also medical literature and social media. We propose a framework for linking social media, medical literature, and EMRs clinical notes using deep learning algorithms. Connecting data sources requires defining a link between them, and our key is finding concepts in the medical text. The National Library of Medicine (NLM) introduces a Unified Medical Language System (UMLS) and we use this system as the foundation of our own system. We recognize social media’s dynamic nature and apply supervised and semi-supervised methodologies to generate concepts. Named entity recognition (NER) allows efficient extraction of information, or entities, from medical literature, and we extend the model to process the EMRs’ clinical notes via transfer learning. The results include an integrated, end-to-end, web-based system solution that unifies social media, literature, and clinical notes, and improves access to medical knowledge for the public and experts.

BackgroundThis study aimed to screen the feature modules and characteristic genes related to ulcerative colitis (UC) and construct a support vector machine (SVM) classifier to distinguish UC patients.MethodsFour datasets that contained UC and control samples were obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) with consistency were screened via the MetaDE method. The weighted gene coexpression network (WGCNA) was used to distinguish significant modules based on the four datasets. The protein–protein interaction network was established based on intersection genes. Enrichment analysis of Gene Ontology (GO) biological processes (BPs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were established based on DAVID. An SVM combined with recursive feature elimination was also applied to construct a disease classifier for the disease diagnosis of UC patients. The efficacy of the SVM classifier was evaluated through receiver operating characteristic curves.ResultsTwelve highly preserved modules were obtained using the WGCNA, and 2009 DEGs with significant consistency were selected using the MetaDE method. Sixteen significantly related GO BPs and 12 KEGG pathways were obtained, such as cytokine-cytokine receptor interaction, cell adhesion molecules, and leukocyte transendothelial migration. Subsequently, 41 genes were used to construct an SVM classifier, such as CXCL1, CCR2, IL1B, and IL1A. The area under the curve (AUC) was 0.999 in the training dataset, whereas the AUC was 0.886, 0.790, and 0.819 in the validation set (GSE65114, GSE37283, and GSE36807, respectively).ConclusionsAn SVM classifier based on feature genes might correctly identify healthy people or UC patients.

This study investigated the effect of a new approach, the support vector machine, as a classifier tool to identify the weeds in corn fields at early growth stage. Image segmentation was done by transforming original color images to gray level images according to the statistical values of red, green, blue components. The Gray Level Co-occurrence Matrix (GLCM) and statistical properties of the histogram from the gray level images were further used to obtain the texture features of the weeds and corn seedlings. These texture features were used in the classification procedure. Principle component analysis was used to select the texture features according to their better contributions to reduce space dimensions. A Support Vector Machine (SVM) classifier was employed to recognize the weeds and the corn seedlings. The results indicated that the SVM classifiers with different feature selections could identify successfully weed-corn with a higher accuracy ranged from 92.31 to 100%. A comparison study of the recognition capabilities of SVM and back-propagation (BP) neural-network classifier using the same data set was conducted. It was found that the SVM classifier provided the best recognition performance with an accuracy of 100%, which exceeded the accuracy of 80% given by the BP classifier. Key words: Corn seedling, weeds, texture, support vector machine, recognize.

A boosted SVM classifier trained by incremental learning and decremental unlearning approach

We perceive the digital watermark detection as classification problem in image processing. We classify watermarked images as positive class whilst unwatermarked images as negative class. Support Vector Machine (SVM) is used as classifier of the watermarked and unwatermarked digital images. Two watermarking schemes i.e. Cox's spread spectrum (SS) and Single Value Decomposition (SVD) are used to embed watermark into digital images. These algorithms are selected based on their different level of robustness to Stirmark attacks. The payload of the watermark used for both algorithms is consistent at certain number of bits. SVM is trained with both the watermarked and unwatermarked images. Receiver Operating Characteristics (ROC) graphs are plotted to assess the statistical detection behavior of both the correlation detector and SVM classifier. We found that straight forward application of SVM leads to generalization problem. We suggest remedies to preprocess the training data in order to achieve substantially better performance from SVM classifier than those resulting from the straightforward application of SVM. Both watermarked and unwatermarked images are attacked under Stirmark and are then tested with the correlation detectors and SVM classifier. A comparison of the ROC of the correlation detectors and SVM classifier is performed to assess the accuracy of SVM classifier relative to correlation detectors. We found that SVM classifier has higher robustness to Stirmark attacks.

An improved SVM classifier based on double chains quantum genetic algorithm and its application in analogue circuit diagnosis

This book chapter presents several natural language processing (NLP) and machine learning (ML) techniques that can help achieve a better medical practice by means of extracting relevant medical information from the wealth of textual data. The chapter describes three major tasks: building intelligent tools that can help in the clinical decision making, tools that can automatically identify relevant medical information from the life-science literature, and tools that can extract semantic relations between medical concepts. Besides introducing and describing these tasks, methodological settings accompanied by representative results obtained on real-life data sets are presented.

Extracting semantic relations from the Quranic Arabic based on Arabic conjunctive patterns