Extracting laboratory test information from biomedical text

<span>In the biomedical field due to tremendous medical research, every year the medical papers generated is very huge. In order to process these tremendous amounts of textual data, the information retrieval techniques are combined with machine learning methods like natural language processing (NLP) for finding the useful insights in data for NLP tasks. In this work, we have addressed the challenges involved in existing NLP techniques like Word2Vec, Doc2Vec, and Biosent2Vec and followed by the traditional classification of articles with Concept2Vec and random forest classification. Concept vector techniques are emerging methods in NLP and in information retrieval systems. Pretrained concept encoders are available in Machine learning, whereas no such exists in biomedical domain. In this paper a proposal on Concept2Vec trained from biomedical text is highlighted. Our work accurately emphasizes on the quality of semantics defined between the medical terms, which can help the medical practitioners in taking errorless decisions. In this work 20 thousand biomedical documents are considered for Concept2Vec embeddings and the proposed approach have shown best concept similarity in terms of relevant measures compared with existing approaches such as Word2Vec, global vectors (GloVe), fastText, and BioSentVec, bidirectional encoder representations from transformers (BERT), biomedical-BERT.</span>

Artificial intelligence has been applied in wildfire science and management since the 1990s, with early applications including neural networks and expert systems. Since then, the field has rapidly progressed congruently with the wide adoption of machine learning (ML) methods in the environmental sciences. Here, we present a scoping review of ML applications in wildfire science and management. Our overall objective is to improve awareness of ML methods among wildfire researchers and managers, as well as illustrate the diverse and challenging range of problems in wildfire science available to ML data scientists. To that end, we first present an overview of popular ML approaches used in wildfire science to date and then review the use of ML in wildfire science as broadly categorized into six problem domains, including (i) fuels characterization, fire detection, and mapping; (ii) fire weather and climate change; (iii) fire occurrence, susceptibility, and risk; (iv) fire behavior prediction; (v) fire effects; and (vi) fire management. Furthermore, we discuss the advantages and limitations of various ML approaches relating to data size, computational requirements, generalizability, and interpretability, as well as identify opportunities for future advances in the science and management of wildfires within a data science context. In total, to the end of 2019, we identified 300 relevant publications in which the most frequently used ML methods across problem domains included random forests, MaxEnt, artificial neural networks, decision trees, support vector machines, and genetic algorithms. As such, there exists opportunities to apply more current ML methods — including deep learning and agent-based learning — in the wildfire sciences, especially in instances involving very large multivariate datasets. We must recognize, however, that despite the ability of ML models to learn on their own, expertise in wildfire science is necessary to ensure realistic modelling of fire processes across multiple scales, while the complexity of some ML methods such as deep learning requires a dedicated and sophisticated knowledge of their application. Finally, we stress that the wildfire research and management communities play an active role in providing relevant, high-quality, and freely available wildfire data for use by practitioners of ML methods.

Software quality indicates how effective and efficient a software is. Various standards need to be used to evaluate software quality. One of the most important internationally accepted standards for measuring software quality is the ISO/IEC 25010 software quality standard. With this standard, the quality of a software product is evaluated with eight different metrics. These are functional suitability, performance, compatibility, usability, reliability, security, maintainability and portability metrics. In this study, we tried to determine the relationship between user feedback and the metrics of the ISO/IEC 25010 software quality standard. Machine learning (ML) and natural language processing (NLP) techniques were used to classify user comments. After the data preprocessing phase, vectors of user comments were extracted with the Tf-Idf method for NLP. As a machine learning method, classification was made using five different models: Extra Trees Classifier (ETC), Gaussian Process Classifier (GPC), MLP Classifier (MLPC), Bernoulli Naive Bayes Classifier (BNBC) and Support Vector Classifier (SVC). Our goal is to show how quality metrics can be classified into multiple classes using user notifications. The data set used has an unbalanced structure, containing 1681 user comments classified by software experts. Synthetic Minority Oversampling Technique (SMOTE) was used to address the imbalance in the dataset. The results were compared by applying the same classification models to unbalanced and balanced data sets. According to the results obtained, the best classification model is the Extra Trees Classifier model, which provides the highest accuracy rate of 87% according to the SMOTE applied data set. The results show that ML and NLP methods can be used effectively in the classification process of software quality metrics.

In the era of artificial intelligence, machine learning methods are successfully used in various fields. Machine learning has attracted extensive attention from investors in the financial market, especially in stock price prediction. However, one argument for the machine learning methods used in stock price prediction is that they are black-box models which are difficult to interpret. In this paper, we focus on the future stock price prediction with the historical stock price by machine learning and deep learning methods, such as support vector machine (SVM), random forest (RF), Bayesian classifier (BC), decision tree (DT), multilayer perceptron (MLP), convolutional neural network (CNN), bi-directional long-short term memory (BiLSTM), the embedded CNN, and the embedded BiLSTM. Firstly, we manually design several financial time series where the future price correlates with the historical stock prices in pre-designed modes, namely the curve-shape-feature (CSF) and the non-curve-shape-feature (NCSF) modes. In the CSF mode, the future prices can be extracted from the curve shapes of the historical stock prices. Conversely, in the NCSF mode, they can’t. Secondly, we apply various algorithms to those pre-designed and real financial time series. We find that the existing machine learning and deep learning algorithms fail in stock price prediction because in the real financial time series, less information of future prices is contained in the CSF mode, and perhaps more information is contained in the NCSF. Various machine learning and deep learning algorithms are good at handling the CSF in historical data, which are successfully applied in image recognition and natural language processing. However, they are inappropriate for stock price prediction on account of the NCSF. Therefore, accurate stock price prediction is the key to successful investment, and new machine learning algorithms handling the NCSF series are needed.

BackgroundMachine learning systems are part of the field of artificial intelligence that automatically learn models from data to make better decisions. Natural language processing (NLP), by using corpora and learning approaches, provides good performance in statistical tasks, such as text classification or sentiment mining.ObjectiveThe primary aim of this systematic review was to summarize and characterize, in methodological and technical terms, studies that used machine learning and NLP techniques for mental health. The secondary aim was to consider the potential use of these methods in mental health clinical practiceMethodsThis systematic review follows the PRISMA (Preferred Reporting Items for Systematic Review and Meta-analysis) guidelines and is registered with PROSPERO (Prospective Register of Systematic Reviews; number CRD42019107376). The search was conducted using 4 medical databases (PubMed, Scopus, ScienceDirect, and PsycINFO) with the following keywords: machine learning, data mining, psychiatry, mental health, and mental disorder. The exclusion criteria were as follows: languages other than English, anonymization process, case studies, conference papers, and reviews. No limitations on publication dates were imposed.ResultsA total of 327 articles were identified, of which 269 (82.3%) were excluded and 58 (17.7%) were included in the review. The results were organized through a qualitative perspective. Although studies had heterogeneous topics and methods, some themes emerged. Population studies could be grouped into 3 categories: patients included in medical databases, patients who came to the emergency room, and social media users. The main objectives were to extract symptoms, classify severity of illness, compare therapy effectiveness, provide psychopathological clues, and challenge the current nosography. Medical records and social media were the 2 major data sources. With regard to the methods used, preprocessing used the standard methods of NLP and unique identifier extraction dedicated to medical texts. Efficient classifiers were preferred rather than transparent functioning classifiers. Python was the most frequently used platform.ConclusionsMachine learning and NLP models have been highly topical issues in medicine in recent years and may be considered a new paradigm in medical research. However, these processes tend to confirm clinical hypotheses rather than developing entirely new information, and only one major category of the population (ie, social media users) is an imprecise cohort. Moreover, some language-specific features can improve the performance of NLP methods, and their extension to other languages should be more closely investigated. However, machine learning and NLP techniques provide useful information from unexplored data (ie, patients’ daily habits that are usually inaccessible to care providers). Before considering It as an additional tool of mental health care, ethical issues remain and should be discussed in a timely manner. Machine learning and NLP methods may offer multiple perspectives in mental health research but should also be considered as tools to support clinical practice.

Machine learning techniques have long been the foundations of speech processing. Bayesian classiflcation, decision trees, unsupervised clustering, the EM algorithm, maximum entropy, etc. are all part of existing speech recognition systems. The success of statistical speech recognition has led to the rise of statistical and empirical methods in natural language processing. Indeed, many of the machine learning techniques used in language processing, from statistical part-of-speech tagging to the noisy channel model for machine translation have roots in work conducted in the speech fleld. However, advances in learning theory and algorithmic machine learning approaches in recent years have led to signiflcant changes in the direction and emphasis of the statistical and learning centered research in natural language processing and made a mark on natural language and speech processing. Approaches such as memory based learning, a range of linear classiflers such as Boosting, SVMs and SNoW and others have been successfully applied to a broad range of natural language problems, and these now inspire new research in speech retrieval and recognition. We have seen an increasingly close collaboration between voice and language processing researchers in some of the shared tasks such as spontaneous speech recognition and understanding, voice data information extraction, and machine translation. The purpose of this special issue was to invite speech and language researchers to communicate with each other, and with the machine learning community on the latest machine learning advances in their work. The call for papers was met with great enthusiasm from the speech and natural language community. Thirty six submissions were received; each paper was reviewed by at least three reviewers. Only ten papers were selected re∞ecting not only some of the best work on machine learning in the areas of natural language and spoken language processing but also what we view as a collection of papers that represent current trends in these areas of research both from the perspective of

Parameter importance assessment improves efficacy of machine learning methods for predicting snow avalanche sites in Leh-Manali Highway, India

Randomized controlled trials (RCTs) provide the strongest evidence for therapeutic interventions and their effects on groups of subjects. However, the large amount of unstructured information in these trials makes it challenging and time-consuming to make decisions and identify important concepts and valid evidence. This study aims to explore methods for automating or semi-automating information extraction from reports of RCT studies. We conducted a systematic search of PubMed, ACM Digital Library, and Web of Science to identify relevant articles published between January 1, 2010, and 2022. We focused on published Natural Language Processing (NLP), machine learning, and deep learning methods that automate or semi-automate key elements of information extraction in the context of RCTs. A total of 26 publications were included, which discussed the automatic extraction of key characteristics of RCTs using various PICO frameworks (PIBOSO and PECODR). Among these publications, 14 (53.8%) extracted key characteristics based on PICO, PIBOSO, and PECODR, while 12 (46.1%) discussed information extraction methods in RCT studies. Common approaches mentioned included word/phrase matching, machine learning algorithms such as binary classification using the Naïve Bayes algorithm and powerful BERT network for feature extraction, support vector machine for data classification, conditional random field, non-machine-dependent automation, and machine learning or deep learning approaches. The lack of publicly available software and limited access to existing software makes it difficult to determine the most powerful information extraction system. However, deep learning models like Transformers and BERT language models have shown better performance in natural language processing.

Machine learning methods, including Deep learnings are popular for data processing. Deep learning methods have shown great promise in applied in natural language processing (NLP) tasks. Text classification is a supervised machine learning task that involves labelled documents to train classifier. Previous works involving machine learning and deep learning methods for text classification have been tested with relatively small- sized data instances. In this paper, we compared the performance of the machine leaning and deep learning algorithms in text classification task. This paper also studied, explored and compared the scalability of these methods with respect to bigger data instances. We used support vector machines (SVM), Logistic regression, Random forest and Naive Bayes Machine leaning algorithms and convolutional neural network (CNN) deep learning method. The task involved a multi-class classification problem involving six (6) classes consisting of six thousand (6,000) data instances with an average of 20 sentences in each data instance. The CNN deep leaning algorithm outperformed all the machine learning algorithms, achieving an accuracy of over 85%. This is because the filter weights are leaning are updated in backward propagation in each epoch, hence, this result in better result compared to the traditional methods.

Integrated phenology and climate in rice yields prediction using machine learning methods

With the ever-growing world of user-generated content in local languages, particularly on communication and social media platforms, the need for emotion analysis and interpretation in such content is on the rise. Hindi being one of the biggest global languages provides a complex and rich language structure and uniqueness that calls for emotion classification in a unique way. This paper outlines a method to categorize Hindi text into pre-established emotional classes through Natural Language Processing and Machine Learning methods. The preprocessing process includes language-dependent operations like handling Devanagari script, removing stopwords, normalization, and TF-IDF vectorization. Various machine learning models like Naïve Bayes, Logistic Regression, Extra Trees Classifier, Ridge Classifier, Random Forest Classifier, and Support Vector Classifier was trained and their results were compared using different performance metrics. Performance metrics measured in terms of the following parameters: F1-score, recall, accuracy, precision, false positives, false negatives, true positives, and true negatives. Among the classifiers, Extra Trees Classifier had the maximum accuracy (0.8497). The research proves the efficacy and applicability of machine learning algorithms in analyzing emotional expressions in Hindi language and lays down a basis for sentiment-aware applications in low-resource languages.

PurposeInjuries are common in sports and can have significant physical, psychological and financial consequences. Machine learning (ML) methods could be used to improve injury prediction and allow proper approaches to injury prevention. The aim of our study was therefore to perform a systematic review of ML methods in sport injury prediction and prevention.MethodsA search of the PubMed database was performed on March 24th 2020. Eligible articles included original studies investigating the role of ML for sport injury prediction and prevention. Two independent reviewers screened articles, assessed eligibility, risk of bias and extracted data. Methodological quality and risk of bias were determined by the Newcastle–Ottawa Scale. Study quality was evaluated using the GRADE working group methodology.ResultsEleven out of 249 studies met inclusion/exclusion criteria. Different ML methods were used (tree-based ensemble methods (n = 9), Support Vector Machines (n = 4), Artificial Neural Networks (n = 2)). The classification methods were facilitated by preprocessing steps (n = 5) and optimized using over- and undersampling methods (n = 6), hyperparameter tuning (n = 4), feature selection (n = 3) and dimensionality reduction (n = 1). Injury predictive performance ranged from poor (Accuracy = 52%, AUC = 0.52) to strong (AUC = 0.87, f1-score = 85%). ConclusionsCurrent ML methods can be used to identify athletes at high injury risk and be helpful to detect the most important injury risk factors. Methodological quality of the analyses was sufficient in general, but could be further improved. More effort should be put in the interpretation of the ML models.

Novel Natural Language Processing and Machine Learning Methods to Characterize Unstructured Patient-Reported Outcomes

Prediction of chronic kidney disease (CKD) has emerged as a useful technique for early detection of at-risk persons and the introduction of appropriate management strategies. Machine learning and data-driven methods have been used in predictive modeling to examine massive databases of patient demographics, medical histories, test findings, and genetic information. These cutting-edge methods allow for the profiling of high-risk patients and the tailoring of healthcare administration approaches. Patient outcomes, complication rates, and healthcare system efficiency may all benefit greatly from CKD screening and prediction. Responsible use of CKD prediction algorithms, however, requires resolving issues with data availability, integration, and ethics. The area of medicine has benefited greatly from the use of Machine Learning (ML) methods, which have played an increasingly central role in illness prediction. In this study, we use a strategy that makes use of ML methods to construct effective tools for predicting the development of CKD. Multiple ML models are trained, and their results are compared using a variety of criteria. We applied five ML methods such as logistic regression (LR), Decision tree (DT), random forest (RF), support vector machine (SVM), and k-nearest neighbor (KNN). The LR and KNN have the highest accuracy with 99%.

A dose deposition matrix (DDM) prediction method using several voxel features and a machine learning (ML) approach is proposed for plan optimization in radiation therapy. Head and lung cases with the inhomogeneous medium are used as training and testing data. The prediction model is a cascade forward backprop neural network where the input is the features of the voxel, including 1) voxel to body surface distance along the beamlet axis, 2) voxel to beamlet axis distance, 3) voxel density, 4) heterogeneity corrected voxel to body surface distance, 5) heterogeneity corrected voxel to beamlet axis, and (6) the dose of voxel obtained from the pencil beam (PB) algorithm. The output is the predicted voxel dose corresponding to a beamlet. The predicted DDM was used for plan optimization (ML method) and compared with the dose of MC-based plan optimization (MC method) and the dose of pencil beam-based plan optimization (PB method). The mean absolute error (MAE) value was calculated for full volume relative to the dose of the MC method to evaluate the overall dose performance of the final plan. For patient with head tumor, the ML method achieves MAE value 0.49 × 10-4 and PB has MAE 1.86 × 10-4. For patient with lung tumor, the ML method has MAE 1.42 × 10-4 and PB has MAE 3.72 × 10-4. The maximum percentage difference in PTV dose coverage (D98) between ML and MC methods is no more than 1.2% for patient with head tumor, while the difference is larger than 10% using the PB method. For patient with lung tumor, the maximum percentage difference in PTV dose coverage (D98) between ML and MC methods is no more than 2.1%, while the difference is larger than 16% using the PB method. In this work, a reliable DDM prediction method is established for plan optimization by applying several voxel features and the ML approach. The results show that the ML method based on voxel features can obtain plans comparable to the MC method and is better than the PB method in achieving accurate dose to the patient, which is helpful for rapid plan optimization and accurate dose calculation. Establishment of a new machine learning method based on the relationship between the voxel and beamlet features for dose deposition matrix prediction in radiation therapy.