News sensitive stock market prediction: literature review and suggestions

Stock market prediction is a challenging task as it requires deep insights for extraction of news events, analysis of historic data, and impact of news events on stock price trends. The challenge is further exacerbated due to the high volatility of stock price trends. However, a detailed overview that discusses the overall context of stock prediction is elusive in literature. To address this research gap, this paper presents a detailed survey. All key terms and phases of generic stock prediction methodology along with challenges, are described. A detailed literature review that covers data preprocessing techniques, feature extraction techniques, prediction techniques, and future directions is presented for news sensitive stock prediction. This work investigates the significance of using structured text features rather than unstructured and shallow text features. It also discusses the use of opinion extraction techniques. In addition, it emphasizes the use of domain knowledge with both approaches of textual feature extraction. Furthermore, it highlights the significance of deep neural network based prediction techniques to capture the hidden relationship between textual and numerical data. This survey is significant and novel as it elaborates a comprehensive framework for stock market prediction and highlights the strengths and weaknesses of existing approaches. It presents a wide range of open issues and research directions that are beneficial for the research community.

Extracting knowledge networks from plant scientific literature: potato tuber flesh color as an exemplary trait

BACKGROUND

Scientific literature carries a wealth of information crucial for research, but only a fraction of it is present as structured information in databases and therefore can be analyzed using traditional data analysis tools. Natural language processing (NLP) is often and successfully employed to support humans by distilling relevant information from large corpora of free text and structuring it in a way that lends itself to further computational analyses. For this pilot, we developed a pipeline that uses NLP on biological literature to produce knowledge networks. We focused on the flesh color of potato, a well-studied trait with known associations, and we investigated whether these knowledge networks can assist us in formulating new hypotheses on the underlying biological processes.

RESULTS

We trained an NLP model based on a manually annotated corpus of 34 full-text potato articles, to recognize relevant biological entities and relationships between them in text (genes, proteins, metabolites and traits). This model detected the number of biological entities with a precision of 97.65% and a recall of 88.91% on the training set. We conducted a time series analysis on 4023 PubMed abstract of plant genetics-based articles which focus on 4 major Solanaceous crops (tomato, potato, eggplant and capsicum), to determine that the networks contained both previously known and contemporaneously unknown leads to subsequently discovered biological phenomena relating to flesh color. A novel time-based analysis of these networks indicates a connection between our trait and a candidate gene (zeaxanthin epoxidase) already two years prior to explicit statements of that connection in the literature.

CONCLUSIONS

Our time-based analysis indicates that network-assisted hypothesis generation shows promise for knowledge discovery, data integration and hypothesis generation in scientific research.

Improved characterisation of clinical text through ontology-based vocabulary expansion

BACKGROUND

Biomedical ontologies contain a wealth of metadata that constitutes a fundamental infrastructural resource for text mining. For several reasons, redundancies exist in the ontology ecosystem, which lead to the same entities being described by several concepts in the same or similar contexts across several ontologies. While these concepts describe the same entities, they contain different sets of complementary metadata. Linking these definitions to make use of their combined metadata could lead to improved performance in ontology-based information retrieval, extraction, and analysis tasks.

RESULTS

We develop and present an algorithm that expands the set of labels associated with an ontology class using a combination of strict lexical matching and cross-ontology reasoner-enabled equivalency queries. Across all disease terms in the Disease Ontology, the approach found 51,362 additional labels, more than tripling the number defined by the ontology itself. Manual validation by a clinical expert on a random sampling of expanded synonyms over the Human Phenotype Ontology yielded a precision of 0.912. Furthermore, we found that annotating patient visits in MIMIC-III with an extended set of Disease Ontology labels led to semantic similarity score derived from those labels being a significantly better predictor of matching first diagnosis, with a mean average precision of 0.88 for the unexpanded set of annotations, and 0.913 for the expanded set.

CONCLUSIONS

Inter-ontology synonym expansion can lead to a vast increase in the scale of vocabulary available for text mining applications. While the accuracy of the extended vocabulary is not perfect, it nevertheless led to a significantly improved ontology-based characterisation of patients from text in one setting. Furthermore, where run-on error is not acceptable, the technique can be used to provide candidate synonyms which can be checked by a domain expert.

Medical informatics labor market analysis using web crawling, web scraping, and text mining

OBJECTIVES

The European University Association (EUA) defines "employability" as a major goal of higher education. Therefore, competence-based orientation is an important aspect of education. The representation of a standardized job profile in the field of medical informatics, which is based on the most common labor market requirements, is fundamental for identifying and conveying the learning goals corresponding to these competences.

METHODS

To identify the most common requirements, we extracted 544 job advertisements from the German job portal, STEPSTONE. This process was conducted via a program we developed in R with the "rvest" library, utilizing web crawling, web extraction, and text mining. After removing duplicates and filtering for jobs that required a bachelor's degree, 147 job advertisements remained, from which we extracted qualification terms. We categorized the terms into six groups: professional expertise, soft skills, teamwork, processes, learning, and problem-solving abilities.

RESULTS

The results showed that only 45% of the terms are related to professional expertise, while 55% are related to soft skills. Studies of employee soft skills have shown similar results. The most prevalent terms were programming, experience, project, and server. Our second major finding is the importance of experience, further underlining how essential practical skills are.

CONCLUSIONS

Previous studies used surveys and narrative descriptions. This is the first study to use web crawling, web extraction, and text mining. Our research shows that soft skills and specialist knowledge carry equal weight. The insights gained from this study may be of assistance in developing curricula for medical informatics.

Monitoring drug trends in the digital environment-New methods, challenges and the opportunities provided by automated approaches

Developments in information technology have impacted on all areas of modern life and in particular facilitated the growth of globalisation in commerce and communication. Within the drugs area this means that both drugs discourse and drug markets have become increasingly digitally enabled. In response to this, new methods are being developed that attempt to research and monitor the digital environment. In this commentary we present three case studies of innovative approaches and related challenges to software-automated data mining of the digital environment: (i) an e-shop finder to detect e-shops offering new psychoactive substances, (ii) scraping of forum data from online discussion boards, (iii) automated sentiment analysis of discussions in online discussion boards. We conclude that the work presented brings opportunities in terms of leveraging data for developing a more timely and granular understanding of the various aspects of drug-use phenomena in the digital environment. In particular, combining the number of e-shops, discussion posts, and sentiments regarding particular substances could be used for ad hoc risk assessments as well as longitudinal drug monitoring and indicate "online popularity". The main challenges of digital data mining involve data representativity and ethical considerations.

Toward assessing clinical trial publications for reporting transparency

OBJECTIVE

To annotate a corpus of randomized controlled trial (RCT) publications with the checklist items of CONSORT reporting guidelines and using the corpus to develop text mining methods for RCT appraisal.

METHODS

We annotated a corpus of 50 RCT articles at the sentence level using 37 fine-grained CONSORT checklist items. A subset (31 articles) was double-annotated and adjudicated, while 19 were annotated by a single annotator and reconciled by another. We calculated inter-annotator agreement at the article and section level using MASI (Measuring Agreement on Set-Valued Items) and at the CONSORT item level using Krippendorff's α. We experimented with two rule-based methods (phrase-based and section header-based) and two supervised learning approaches (support vector machine and BioBERT-based neural network classifiers), for recognizing 17 methodology-related items in the RCT Methods sections.

RESULTS

We created CONSORT-TM consisting of 10,709 sentences, 4,845 (45%) of which were annotated with 5,246 labels. A median of 28 CONSORT items (out of possible 37) were annotated per article. Agreement was moderate at the article and section levels (average MASI: 0.60 and 0.64, respectively). Agreement varied considerably among individual checklist items (Krippendorff's α= 0.06-0.96). The model based on BioBERT performed best overall for recognizing methodology-related items (micro-precision: 0.82, micro-recall: 0.63, micro-F1: 0.71). Combining models using majority vote and label aggregation further improved precision and recall, respectively.

CONCLUSION

Our annotated corpus, CONSORT-TM, contains more fine-grained information than earlier RCT corpora. Low frequency of some CONSORT items made it difficult to train effective text mining models to recognize them. For the items commonly reported, CONSORT-TM can serve as a testbed for text mining methods that assess RCT transparency, rigor, and reliability, and support methods for peer review and authoring assistance. Minor modifications to the annotation scheme and a larger corpus could facilitate improved text mining models. CONSORT-TM is publicly available at https://github.com/kilicogluh/CONSORT-TM.

The key successful factors of video and mobile game crowdfunding projects using a lexicon-based feature selection approach

The emergence of crowdfunding has given many capital demanders a new fund-raising channel, but the overall project success rate is very low. Many scholars have begun to discover key suscessful factors of crowdfunding projects. Previous studies have used questionnaires survey to identify important project features. In addition to requiring a lot of manpower and time, there may also be sampling bias. Moreover, related studies also reported that the project description will affect the success of the crowdfunding project, but there is no research to tell fundraisers which success factors should be included in the content of the project description. Besides, in recent years, game crowdfunding projects have been attracted lots of attention in terms of total fundraising amount and number of projects. Moreover, in traditional feature selection and text mining approaches, the selected terms are un-organized and hard to be explained. Therefore, this study will focus on real video and mobile game project descriptions to replace conventional questionnaires. To solve these issues, we present a lexicon-based feature selection method. We attempt to define "content features" and build lexicons to determine the attributes' values. Three feature selection methods including decision tree (DT), Least Absolute Shrinkage and Selection Operator (LASSO), and support vector machine-recursive feature elimination (SVM-RFE) will be employed to find organized candidate key successful factors. Then, support vector machines (SVM) will be used to evaluate the performances of candidate feature subsets. Finally, this study has identified the key successful factors for video and mobile games, respectively. Based on the experimental results, we can give fundraisers some useful suggestions to improve the success rate of crowdfunding projects.

Natural language processing for urban research: A systematic review

Natural language processing (NLP) has shown potential as a promising tool to exploit under-utilized urban data sources. This paper presents a systematic review of urban studies published in peer-reviewed journals and conference proceedings that adopted NLP. The review suggests that the application of NLP in studying cities is still in its infancy. Current applications fell into five areas: urban governance and management, public health, land use and functional zones, mobility, and urban design. NLP demonstrates the advantages of improving the usability of urban big data sources, expanding study scales, and reducing research costs. On the other hand, to take advantage of NLP, urban researchers face challenges of raising good research questions, overcoming data incompleteness, inaccessibility, and non-representativeness, immature NLP techniques, and computational skill requirements. This review is among the first efforts intended to provide an overview of existing applications and challenges for advancing urban research through the adoption of NLP.

NewsMeSH: A new classifier designed to annotate health news with MeSH headings

MOTIVATION

In the age of big data, the amount of scientific information available online dwarfs the ability of current tools to support researchers in locating and securing access to the necessary materials. Well-structured open data and the smart systems that make the appropriate use of it are invaluable and can help health researchers and professionals to find the appropriate information by, e.g., configuring the monitoring of information or refining a specific query on a disease.

METHODS

We present an automated text classifier approach based on the MEDLINE/MeSH thesaurus, trained on the manual annotation of more than 26 million expert-annotated scientific abstracts. The classifier was developed tailor-fit to the public health and health research domain experts, in the light of their specific challenges and needs. We have applied the proposed methodology on three specific health domains: the Coronavirus, Mental Health and Diabetes, considering the pertinence of the first, and the known relations with the other two health topics.

RESULTS

A classifier is trained on the MEDLINE dataset that can automatically annotate text, such as scientific articles, news articles or medical reports with relevant concepts from the MeSH thesaurus.

CONCLUSIONS

The proposed text classifier shows promising results in the evaluation of health-related news. The application of the developed classifier enables the exploration of news and extraction of health-related insights, based on the MeSH thesaurus, through a similar workflow as in the usage of PubMed, with which most health researchers are familiar.

Persian sentiment analysis of an online store independent of pre-processing using convolutional neural network with fastText embeddings

Sentiment analysis plays a key role in companies, especially stores, and increasing the accuracy in determining customers' opinions about products assists to maintain their competitive conditions. We intend to analyze the users' opinions on the website of the most immense online store in Iran; Digikala. However, the Persian language is unstructured which makes the pre-processing stage very difficult and it is the main problem of sentiment analysis in Persian. What exacerbates this problem is the lack of available libraries for Persian pre-processing, while most libraries focus on English. To tackle this, approximately 3 million reviews were gathered in Persian from the Digikala website using web-mining techniques, and the fastText method was used to create a word embedding. It was assumed that this would dramatically cut down on the need for text pre-processing through the skip-gram method considering the position of the words in the sentence and the words' relations to each other. Another word embedding has been created using the TF-IDF in parallel with fastText to compare their performance. In addition, the results of the Convolutional Neural Network (CNN), BiLSTM, Logistic Regression, and Naïve Bayes models have been compared. As a significant result, we obtained 0.996 AUC and 0.956 F-score using fastText and CNN. In this article, not only has it been demonstrated to what extent it is possible to be independent of pre-processing but also the accuracy obtained is better than other researches done in Persian. Avoiding complex text preprocessing is also important for other languages since most text preprocessing algorithms have been developed for English and cannot be used for other languages. The created word embedding due to its high accuracy and independence of pre-processing has other applications in Persian besides sentiment analysis.

Clinical notes as prognostic markers of mortality associated with diabetes mellitus following critical care: A retrospective cohort analysis using machine learning and unstructured big data

BACKGROUND

Clinical notes are ubiquitous resources offering potential value in optimizing critical care via data mining technologies.

OBJECTIVE

To determine the predictive value of clinical notes as prognostic markers of 1-year all-cause mortality among people with diabetes following critical care.

MATERIALS AND METHODS

Mortality of diabetes patients were predicted using three cohorts of clinical text in a critical care database, written by physicians (n = 45253), nurses (159027), and both (n = 204280). Natural language processing was used to pre-process text documents and LASSO-regularized logistic regression models were trained and tested. Confusion matrix metrics of each model were calculated and AUROC estimates between models were compared. All predictive words and corresponding coefficients were extracted. Outcome probability associated with each text document was estimated.

RESULTS

Models built on clinical text of physicians, nurses, and the combined cohort predicted mortality with AUROC of 0.996, 0.893, and 0.922, respectively. Predictive performance of the models significantly differed from one another whereas inter-rater reliability ranged from substantial to almost perfect across them. Number of predictive words with non-zero coefficients were 3994, 8159, and 10579, respectively, in the models of physicians, nurses, and the combined cohort. Physicians' and nursing notes, both individually and when combined, strongly predicted 1-year all-cause mortality among people with diabetes following critical care.

CONCLUSION

Clinical notes of physicians and nurses are strong and novel prognostic markers of diabetes-associated mortality in critical care, offering potentially generalizable and scalable applications. Clinical text-derived personalized risk estimates of prognostic outcomes such as mortality could be used to optimize patient care.

Applying machine learning, text mining, and spatial analysis techniques to develop a highway-railroad grade crossing consolidation model

The consolidation of Highway-Railroad Grade Crossing (HRGC) is one of the effective approaches to decrease the number of crashes between trains and vehicles. From 2015-2019, there were 57 HRGC crashes at crossings in East Baton Rouge Parish (EBRP), resulting in thirteen injuries with $346,875 cost of vehicle damages. Consolidation programs help to close redundant crossings and thereby decrease the crash risks; however, it is difficult to find the best crossing in a neighborhood for closure. In our previous research working on HRGC consolidation models in 2019, from among four Machine Learning algorithms, eXtreme Gradient Boosting (XGboost) performed better in HRGC prediction models. In continuation of our previous studies on developing a HRGC prediction model, this research employed Text Mining Techniques, and Geospatial Analysis in addition to the XGboost Machine Learning algorithm. The aim was to develop a consolidation model that is customized for local implementation. The results indicated an overall accuracy of 88 % for the proposed model. The relative importance of the variables input to the model was also reported and offers an in-depth understanding of the model's behavior. Considering the different correlation threshold, a sensitivity analysis was also performed on different aggregation gain values. Subsequently, it resulted in the development of a simplified model utilizing 14 variables, with aggregated gain values of 95 % and a correlation threshold of 0.5. Based on this model, 15 % of current highway-rail grade crossings should be closed.

Drug repurposing for COVID-19 via knowledge graph completion

OBJECTIVE

To discover candidate drugs to repurpose for COVID-19 using literature-derived knowledge and knowledge graph completion methods.

METHODS

We propose a novel, integrative, and neural network-based literature-based discovery (LBD) approach to identify drug candidates from PubMed and other COVID-19-focused research literature. Our approach relies on semantic triples extracted using SemRep (via SemMedDB). We identified an informative and accurate subset of semantic triples using filtering rules and an accuracy classifier developed on a BERT variant. We used this subset to construct a knowledge graph, and applied five state-of-the-art, neural knowledge graph completion algorithms (i.e., TransE, RotatE, DistMult, ComplEx, and STELP) to predict drug repurposing candidates. The models were trained and assessed using a time slicing approach and the predicted drugs were compared with a list of drugs reported in the literature and evaluated in clinical trials. These models were complemented by a discovery pattern-based approach.

RESULTS

Accuracy classifier based on PubMedBERT achieved the best performance (F1 = 0.854) in identifying accurate semantic predications. Among five knowledge graph completion models, TransE outperformed others (MR = 0.923, Hits@1 = 0.417). Some known drugs linked to COVID-19 in the literature were identified, as well as others that have not yet been studied. Discovery patterns enabled identification of additional candidate drugs and generation of plausible hypotheses regarding the links between the candidate drugs and COVID-19. Among them, five highly ranked and novel drugs (i.e., paclitaxel, SB 203580, alpha 2-antiplasmin, metoclopramide, and oxymatrine) and the mechanistic explanations for their potential use are further discussed.

CONCLUSION

We showed that a LBD approach can be feasible not only for discovering drug candidates for COVID-19, but also for generating mechanistic explanations. Our approach can be generalized to other diseases as well as to other clinical questions. Source code and data are available at https://github.com/kilicogluh/lbd-covid.

Mining topic and sentiment dynamics in physician rating websites during the early wave of the COVID-19 pandemic: Machine learning approach

INTRODUCTION

An increasing number of patients are voicing their opinions and expectations about the quality of care in online forums and on physician rating websites (PRWs). This paper analyzes patient online reviews (PORs) to identify emerging and fading topics and sentiment trends in PRWs during the early stage of the COVID-19 outbreak.

METHODS

Text data were collected, including 55,612 PORs of 3430 doctors from three popular PRWs in the United States (RateMDs, HealthGrades, and Vitals) from March 01 to June 27, 2020. An improved latent Dirichlet allocation (LDA)-based topic modeling (topic coherence-based LDA [TCLDA]), manual annotation, and sentiment analysis tool were applied to extract a suitable number of topics, generate corresponding keywords, assign topic names, and determine trends in the extracted topics and specific emotions.

RESULTS

According to the coherence value and manual annotation, the identified taxonomy includes 30 topics across high-rank and low-rank disease categories. The emerging topics in PRWs focus mainly on themes such as treatment experience, policy implementation regarding epidemic control measures, individuals' attitudes toward the pandemic, and mental health across high-rank diseases. In contrast, the treatment process and experience during COVID-19, awareness and COVID-19 control measures, and COVID-19 deaths, fear, and stress were the most popular themes for low-rank diseases. Panic buying and daily life impact, treatment processes, and bedside manner were the fading themes across high-rank diseases. In contrast, provider attitude toward patients during the pandemic, detection at public transportation, passenger, travel bans and warnings, and materials supplies and society support during COVID-19 were the most fading themes across low-rank diseases. Regarding sentiment analysis, negative emotions (fear, anger, and sadness) prevail during the early wave of the COVID-19.

CONCLUSION

Mining topic dynamics and sentiment trends in PRWs may provide valuable knowledge of patients' opinions during the COVID-19 crisis. Policymakers should consider these PORs and develop global healthcare policies and surveillance systems through monitoring PRWs. The findings of this study identify research gaps in the areas of e-health and text mining and offer future research directions.

Attitude of Chinese public towards municipal solid waste sorting policy: A text mining study

With the acceleration of urban development, the amount of municipal solid waste (MSW) has increased dramatically. In order to recycle MSW more efficiently, a compulsory policy of sorting MSW has been enacted in China. According to the existing literature, attitude is an important factor affecting public's MSW sorting behavior. To explore the Chinese residents' emotional tendency towards the MSW sorting policy, this study analyzed the data of Sina Weibo users and their comments on related popular posts. Meanwhile, text mining technology was employed to analyze the collected data. Results showed that although a large proportion of the Chinese public has a positive attitude towards the MSW sorting policy, the proportion of people with negative emotions reached nearly half. In addition, it was found that the Chinese people in different regions pay different attentions to the MSW sorting policy. Results further revealed that the main reasons for the public's negative emotions were fines, MSW sorting rules, fees, timing of throwing waste, and irregular recycling procedures. By providing the public sentiment analysis of MSW sorting, this study can serve as a policy guide for practitioners and policy-makers to link current research areas into social development.

MultiGBS: A multi-layer graph approach to biomedical summarization

Automatic text summarization methods generate a shorter version of the input text to assist the reader in gaining a quick yet informative gist. Existing text summarization methods generally focus on a single aspect of text when selecting sentences, causing the potential loss of essential information. In this study, we propose a domain-specific method that models a document as a multi-layer graph to enable multiple features of the text to be processed at the same time. The features we used in this paper are word similarity, semantic similarity, and co-reference similarity, which are modelled as three different layers. The unsupervised method selects sentences from the multi-layer graph based on the MultiRank algorithm and the number of concepts. The proposed MultiGBS algorithm employs UMLS and extracts the concepts and relationships using different tools such as SemRep, MetaMap, and OGER. Extensive evaluation by ROUGE and BERTScore shows increased F-measure values.

The nurse COVID and historical epidemics literature repository: Development, description, and summary

Background

During COVID-19, a Kaggle challenge was issued to data scientists to leverage text mining to provide high-level summaries of full-text articles in the COVID-19 Open Research Dataset (CORD-19) data set, a data set containing articles around COVID-19 and other epidemics. A question was asked: “What if nursing had something similar?”

Purpose

Describe the development and function of the Nursing COVID and Historical Epidemic Literature and describe high-level summaries of abstracts within the repository.

Method

Nurse-specific literature was abstracted from two data sets: CORD-19 and LitCOVID. LitCOVID is a data set containing the most up-to-date literature around COVID-19. Multiple text mining algorithms were utilized to provide summaries of the articles.

Discussion

As of July 2020, the repository contains 760 articles. Summaries indicate the importance of psychological support for nurses and of high-impact rapid education.

Conclusion

To our knowledge, this repository is the only repository specific for nursing that utilizes text mining to provide summaries.

UrbangEnCy: An emergency events dataset based on citizen sensors for monitoring urban scenarios in Ecuador

Recently, the use of the citizen-sensors (people generating and sharing real data by social media) for detecting and disseminating emergency events in real-time have shown a considerable increase because people at the place of the event, as well as elsewhere, can quickly post relevant information on this type of alerts. Here, we present an emergency events dataset called UrbangEnCy. The dataset contains over 25500 texts in Spanish posted on Twitter from January 19th to August 19th, 2020, with emergencies and non-emergencies related content in Ecuador. We obtained, cleaned and, filtered these tweets and, then we selected the location and temporal data as well as tweet content. Besides, the data set includes annotations regarding the type of tweet (emergency / non-emergency) as well as additional nomenclature used to describe emergencies in the Center for immediate response service to emergencies (ECU 911) of Ecuador and international emergency services agencies (ESAs). UrbangEnCy dataset facilitates evaluating data science performance, machine learning, and natural language processing algorithms used with supervised and unsupervised problems re- related to text mining and pattern recognition. The dataset is freely and publicly available at https://doi.org/10.17632/4x37zz82k8.

An automated approach to identify scientific publications reporting pharmacokinetic parameters

Pharmacokinetic (PK) predictions of new chemical entities are aided by prior knowledge from other compounds. The development of robust algorithms that improve preclinical and clinical phases of drug development remains constrained by the need to search, curate and standardise PK information across the constantly-growing scientific literature. The lack of centralised, up-to-date and comprehensive repositories of PK data represents a significant limitation in the drug development pipeline.In this work, we propose a machine learning approach to automatically identify and characterise scientific publications reporting PK parameters from in vivo data, providing a centralised repository of PK literature. A dataset of 4,792 PubMed publications was labelled by field experts depending on whether in vivo PK parameters were estimated in the study. Different classification pipelines were compared using a bootstrap approach and the best-performing architecture was used to develop a comprehensive and automatically-updated repository of PK publications. The best-performing architecture encoded documents using unigram features and mean pooling of BioBERT embeddings obtaining an F1 score of 83.8% on the test set. The pipeline retrieved over 121K PubMed publications in which in vivo PK parameters were estimated and it was scheduled to perform weekly updates on newly published articles. All the relevant documents were released through a publicly available web interface (https://app.pkpdai.com) and characterised by the drugs, species and conditions mentioned in the abstract, to facilitate the subsequent search of relevant PK data. This automated, open-access repository can be used to accelerate the search and comparison of PK results, curate ADME datasets, and facilitate subsequent text mining tasks in the PK domain.

Analysis of associations between emotions and activities of drug users and their addiction recovery tendencies from social media posts using structural equation modeling

Background

Addiction to drugs and alcohol constitutes one of the significant factors underlying the decline in life expectancy in the US. Several context-specific reasons influence drug use and recovery. In particular emotional distress, physical pain, relationships, and self-development efforts are known to be some of the factors associated with addiction recovery. Unfortunately, many of these factors are not directly observable and quantifying, and assessing their impact can be difficult. Based on social media posts of users engaged in substance use and recovery on the forum Reddit, we employed two psycholinguistic tools, Linguistic Inquiry and Word Count and Empath and activities of substance users on various Reddit sub-forums to analyze behavior underlining addiction recovery and relapse. We then employed a statistical analysis technique called structural equation modeling to assess the effects of these latent factors on recovery and relapse.

Results

We found that both emotional distress and physical pain significantly influence addiction recovery behavior. Self-development activities and social relationships of the substance users were also found to enable recovery. Furthermore, within the context of self-development activities, those that were related to influencing the mental and physical well-being of substance users were found to be positively associated with addiction recovery. We also determined that lack of social activities and physical exercise can enable a relapse. Moreover, geography, especially life in rural areas, appears to have a greater correlation with addiction relapse.

Conclusions

The paper describes how observable variables can be extracted from social media and then be used to model important latent constructs that impact addiction recovery and relapse. We also report factors that impact self-induced addiction recovery and relapse. To the best of our knowledge, this paper represents the first use of structural equation modeling of social media data with the goal of analyzing factors influencing addiction recovery.

A comprehensive study of mobility functioning information in clinical notes: Entity hierarchy, corpus annotation, and sequence labeling

BACKGROUND

Secondary use of Electronic Health Records (EHRs) has mostly focused on health conditions (diseases and drugs). Function is an important health indicator in addition to morbidity and mortality. Nevertheless, function has been overlooked in accessing patients' health status. The World Health Organization (WHO)'s International Classification of Functioning, Disability and Health (ICF) is considered the international standard for describing and coding function and health states. We pioneer the first comprehensive analysis and identification of functioning concepts in the Mobility domain of the ICF.

RESULTS

Using physical therapy notes at the National Institutes of Health's Clinical Center, we induced a hierarchical order of mobility-related entities including 5 entities types, 3 relations, 8 attributes, and 33 attribute values. Two domain experts manually curated a gold standard corpus of 14,281 nested entity mentions from 400 clinical notes. Inter-annotator agreement (IAA) of exact matching averaged 92.3 % F1-score on mention text spans, and 96.6 % Cohen's kappa on attributes assignments. A high-performance Ensemble machine learning model for named entity recognition (NER) was trained and evaluated using the gold standard corpus. Average F1-score on exact entity matching of our Ensemble method (84.90 %) outperformed popular NER methods: Conditional Random Field (80.4 %), Recurrent Neural Network (81.82 %), and Bidirectional Encoder Representations from Transformers (82.33 %).

CONCLUSIONS

The results of this study show that mobility functioning information can be reliably captured from clinical notes once adequate resources are provided for sequence labeling methods. We expect that functioning concepts in other domains of the ICF can be identified in similar fashion.

Topics and trends in Mountain Livestock Farming research: a text mining approach

Pasture-based and small-scale livestock farming systems are the main source of livelihood in the mountain primary sector, ensuring socioeconomic sustainability and biodiversity in rural communities throughout Europe and beyond. Mountain livestock farming (MLF) has attracted substantial research efforts from a wide variety of scientific communities worldwide. In this study, the use of text mining and topic modelling analysis drew a detailed picture of the main research topics dealing with MLF and their trends over the last four decades. The final data corpus used for the analysis counted 2 679 documents, of which 92% were peer-reviewed scientific publications. The number of scientific outputs in MLF doubled every 10 years since 1980. Text mining found that milk, goat and sheep were the terms with the highest weighed frequency in the data corpus. Ten meaningful topics were identified by topic analysis: T1-Livestock management and vegetation dynamics; T2-Animal health and epidemiology; T3-Methodological studies on cattle; T4-Production system and sustainability; T5-Methodological studies; T6-Wildlife and conservation studies; T7-Reproduction and performance; T8-Dairy/meat production and quality; T9-Land use and its change and T10-Genetic/genomic studies. A hierarchical clustering analysis was performed to explore the interrelationships among topics, and three main clusters were identified: the first focused on sustainability, conservation and socioeconomic aspects (T4; T6 and T9), the second was related to food production and quality (T7 and T8) and the last one considered methodological studies on mountain flora and fauna (T1; T2; T3; T5 and T10). The 10 topics identified represent a useful and a starting source of information for further and more detailed analysis (e.g. systematic review) of specific research or geographical areas. A truly holistic and interdisciplinary research approach is needed to identify drivers of change and to understand current and future challenges faced by livestock farming in mountain areas.

Aligning text mining and machine learning algorithms with best practices for study selection in systematic literature reviews

BACKGROUND

Despite existing research on text mining and machine learning for title and abstract screening, the role of machine learning within systematic literature reviews (SLRs) for health technology assessment (HTA) remains unclear given lack of extensive testing and of guidance from HTA agencies. We sought to address two knowledge gaps: to extend ML algorithms to provide a reason for exclusion-to align with current practices-and to determine optimal parameter settings for feature-set generation and ML algorithms.

METHODS

We used abstract and full-text selection data from five large SLRs (n = 3089 to 12,769 abstracts) across a variety of disease areas. Each SLR was split into training and test sets. We developed a multi-step algorithm to categorize each citation into the following categories: included; excluded for each PICOS criterion; or unclassified. We used a bag-of-words approach for feature-set generation and compared machine learning algorithms using support vector machines (SVMs), naïve Bayes (NB), and bagged classification and regression trees (CART) for classification. We also compared alternative training set strategies: using full data versus downsampling (i.e., reducing excludes to balance includes/excludes because machine learning algorithms perform better with balanced data), and using inclusion/exclusion decisions from abstract versus full-text screening. Performance comparisons were in terms of specificity, sensitivity, accuracy, and matching the reason for exclusion.

RESULTS

The best-fitting model (optimized sensitivity and specificity) was based on the SVM algorithm using training data based on full-text decisions, downsampling, and excluding words occurring fewer than five times. The sensitivity and specificity of this model ranged from 94 to 100%, and 54 to 89%, respectively, across the five SLRs. On average, 75% of excluded citations were excluded with a reason and 83% of these citations matched the reviewers' original reason for exclusion. Sensitivity significantly improved when both downsampling and abstract decisions were used.

CONCLUSIONS

ML algorithms can improve the efficiency of the SLR process and the proposed algorithms could reduce the workload of a second reviewer by identifying exclusions with a relevant PICOS reason, thus aligning with HTA guidance. Downsampling can be used to improve study selection, and improvements using full-text exclusions have implications for a learn-as-you-go approach.

Mind the gap: Developments in autonomous driving research and the sustainability challenge

Scientific knowledge on autonomous-driving technology is expanding at a faster-than-ever pace. As a result, the likelihood of incurring information overload is particularly notable for researchers, who can struggle to overcome the gap between information processing requirements and information processing capacity. We address this issue by adopting a multi-granulation approach to latent knowledge discovery and synthesis in large-scale research domains. The proposed methodology combines citation-based community detection methods and topic modelling techniques to give a concise but comprehensive overview of how the autonomous vehicle (AV) research field is conceptually structured. Thirteen core thematic areas are extracted and presented by mining the large data-rich environments resulting from 50 years of AV research. The analysis demonstrates that this research field is strongly oriented towards examining the technological developments needed to enable the widespread rollout of AVs, whereas it largely overlooks the wide-ranging sustainability implications of this sociotechnical transition. On account of these findings, we call for a broader engagement of AV researchers with the sustainability concept and we invite them to increase their commitment to conducting systematic investigations into the sustainability of AV deployment. Sustainability research is urgently required to produce an evidence-based understanding of what new sociotechnical arrangements are needed to ensure that the systemic technological change introduced by AV-based transport systems can fulfill societal functions while meeting the urgent need for more sustainable transport solutions.

Decoding semi-automated title-abstract screening: findings from a convenience sample of reviews

BACKGROUND

We evaluated the benefits and risks of using the Abstrackr machine learning (ML) tool to semi-automate title-abstract screening and explored whether Abstrackr's predictions varied by review or study-level characteristics.

METHODS

For a convenience sample of 16 reviews for which adequate data were available to address our objectives (11 systematic reviews and 5 rapid reviews), we screened a 200-record training set in Abstrackr and downloaded the relevance (relevant or irrelevant) of the remaining records, as predicted by the tool. We retrospectively simulated the liberal-accelerated screening approach. We estimated the time savings and proportion missed compared with dual independent screening. For reviews with pairwise meta-analyses, we evaluated changes to the pooled effects after removing the missed studies. We explored whether the tool's predictions varied by review and study-level characteristics.

RESULTS

Using the ML-assisted liberal-accelerated approach, we wrongly excluded 0 to 3 (0 to 14%) records that were included in the final reports, but saved a median (IQR) 26 (9, 42) h of screening time. One missed study was included in eight pairwise meta-analyses in one systematic review. The pooled effect for just one of those meta-analyses changed considerably (from MD (95% CI) - 1.53 (- 2.92, - 0.15) to - 1.17 (- 2.70, 0.36)). Of 802 records in the final reports, 87% were correctly predicted as relevant. The correctness of the predictions did not differ by review (systematic or rapid, P = 0.37) or intervention type (simple or complex, P = 0.47). The predictions were more often correct in reviews with multiple (89%) vs. single (83%) research questions (P = 0.01), or that included only trials (95%) vs. multiple designs (86%) (P = 0.003). At the study level, trials (91%), mixed methods (100%), and qualitative (93%) studies were more often correctly predicted as relevant compared with observational studies (79%) or reviews (83%) (P = 0.0006). Studies at high or unclear (88%) vs. low risk of bias (80%) (P = 0.039), and those published more recently (mean (SD) 2008 (7) vs. 2006 (10), P = 0.02) were more often correctly predicted as relevant.

CONCLUSION

Our screening approach saved time and may be suitable in conditions where the limited risk of missing relevant records is acceptable. Several of our findings are paradoxical and require further study to fully understand the tasks to which ML-assisted screening is best suited. The findings should be interpreted in light of the fact that the protocol was prepared for the funder, but not published a priori. Because we used a convenience sample, the findings may be prone to selection bias. The results may not be generalizable to other samples of reviews, ML tools, or screening approaches. The small number of missed studies across reviews with pairwise meta-analyses hindered strong conclusions about the effect of missed studies on the results and conclusions of systematic reviews.