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Poalelungi DG, Musat CL, Fulga A, Neagu M, Neagu AI, Piraianu AI, Fulga I. Advancing Patient Care: How Artificial Intelligence Is Transforming Healthcare. J Pers Med 2023; 13:1214. [PMID: 37623465 PMCID: PMC10455458 DOI: 10.3390/jpm13081214] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
Artificial Intelligence (AI) has emerged as a transformative technology with immense potential in the field of medicine. By leveraging machine learning and deep learning, AI can assist in diagnosis, treatment selection, and patient monitoring, enabling more accurate and efficient healthcare delivery. The widespread implementation of AI in healthcare has the role to revolutionize patients' outcomes and transform the way healthcare is practiced, leading to improved accessibility, affordability, and quality of care. This article explores the diverse applications and reviews the current state of AI adoption in healthcare. It concludes by emphasizing the need for collaboration between physicians and technology experts to harness the full potential of AI.
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Affiliation(s)
- Diana Gina Poalelungi
- Saint Apostle Andrew Emergency County Clinical Hospital, 177 Brailei st., 800578 Galati, Romania; (D.G.P.); (M.N.); (A.I.P.); (I.F.)
| | - Carmina Liana Musat
- Saint Apostle Andrew Emergency County Clinical Hospital, 177 Brailei st., 800578 Galati, Romania; (D.G.P.); (M.N.); (A.I.P.); (I.F.)
- Faculty of Medicine and Pharmacy, Dunarea de Jos University of Galati, 35 AI Cuza st., 800010 Galati, Romania;
| | - Ana Fulga
- Saint Apostle Andrew Emergency County Clinical Hospital, 177 Brailei st., 800578 Galati, Romania; (D.G.P.); (M.N.); (A.I.P.); (I.F.)
- Faculty of Medicine and Pharmacy, Dunarea de Jos University of Galati, 35 AI Cuza st., 800010 Galati, Romania;
| | - Marius Neagu
- Saint Apostle Andrew Emergency County Clinical Hospital, 177 Brailei st., 800578 Galati, Romania; (D.G.P.); (M.N.); (A.I.P.); (I.F.)
- Faculty of Medicine and Pharmacy, Dunarea de Jos University of Galati, 35 AI Cuza st., 800010 Galati, Romania;
| | - Anca Iulia Neagu
- Faculty of Medicine and Pharmacy, Dunarea de Jos University of Galati, 35 AI Cuza st., 800010 Galati, Romania;
- ‘Saint John’ Clinical Emergency Hospital for Children, 800487 Galati, Romania
| | - Alin Ionut Piraianu
- Saint Apostle Andrew Emergency County Clinical Hospital, 177 Brailei st., 800578 Galati, Romania; (D.G.P.); (M.N.); (A.I.P.); (I.F.)
- Faculty of Medicine and Pharmacy, Dunarea de Jos University of Galati, 35 AI Cuza st., 800010 Galati, Romania;
| | - Iuliu Fulga
- Saint Apostle Andrew Emergency County Clinical Hospital, 177 Brailei st., 800578 Galati, Romania; (D.G.P.); (M.N.); (A.I.P.); (I.F.)
- Faculty of Medicine and Pharmacy, Dunarea de Jos University of Galati, 35 AI Cuza st., 800010 Galati, Romania;
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Mehrpour O, Saeedi F, Nakhaee S, Tavakkoli Khomeini F, Hadianfar A, Amirabadizadeh A, Hoyte C. Comparison of decision tree with common machine learning models for prediction of biguanide and sulfonylurea poisoning in the United States: an analysis of the National Poison Data System. BMC Med Inform Decis Mak 2023; 23:60. [PMID: 37024869 PMCID: PMC10080923 DOI: 10.1186/s12911-022-02095-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 12/26/2022] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Biguanides and sulfonylurea are two classes of anti-diabetic medications that have commonly been prescribed all around the world. Diagnosis of biguanide and sulfonylurea exposures is based on history taking and physical examination; thus, physicians might misdiagnose these two different clinical settings. We aimed to conduct a study to develop a model based on decision tree analysis to help physicians better diagnose these poisoning cases. METHODS The National Poison Data System was used for this six-year retrospective cohort study.The decision tree model, common machine learning models multi layers perceptron, stochastic gradient descent (SGD), Adaboosting classiefier, linear support vector machine and ensembling methods including bagging, voting and stacking methods were used. The confusion matrix, precision, recall, specificity, f1-score, and accuracy were reported to evaluate the model's performance. RESULTS Of 6183 participants, 3336 patients (54.0%) were identified as biguanides exposures, and the remaining were those with sulfonylureas exposures. The decision tree model showed that the most important clinical findings defining biguanide and sulfonylurea exposures were hypoglycemia, abdominal pain, acidosis, diaphoresis, tremor, vomiting, diarrhea, age, and reasons for exposure. The specificity, precision, recall, f1-score, and accuracy of all models were greater than 86%, 89%, 88%, and 88%, respectively. The lowest values belong to SGD model. The decision tree model has a sensitivity (recall) of 93.3%, specificity of 92.8%, precision of 93.4%, f1_score of 93.3%, and accuracy of 93.3%. CONCLUSION Our results indicated that machine learning methods including decision tree and ensembling methods provide a precise prediction model to diagnose biguanides and sulfonylureas exposure.
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Affiliation(s)
- Omid Mehrpour
- Data Science Institute, Southern Methodist University, Dallas, TX, USA.
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand, Iran.
| | - Farhad Saeedi
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand, Iran
- Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran
| | - Samaneh Nakhaee
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand, Iran
| | | | - Ali Hadianfar
- Department of Epidemiology and Biostatistics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Amirabadizadeh
- Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Mehrpour O, Nakhaee S, Saeedi F, Valizade B, Lotfi E, Nawaz MH. Utility of artificial intelligence to identify antihyperglycemic agents poisoning in the USA: introducing a practical web application using National Poison Data System (NPDS). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:57801-57810. [PMID: 36973614 DOI: 10.1007/s11356-023-26605-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/18/2023] [Indexed: 05/10/2023]
Abstract
Clinical effects of antihyperglycemic agents poisoning may overlap each other. So, distinguishing exposure to these pharmaceutical drugs may take work. This study examined the application of machine learning techniques in identifying antihyperglycemic agent exposure using the national poisoning database in the USA. In this study, the data of single exposure due to Biguanides and Sulfonylureas (n=6183) was requested from the National Poison Data System (NPDS) for 2014-2018. We have tried five machine learning models (random forest classifier, k-nearest neighbors, Xgboost classifier, logistic regression, neural network Keras). For the multiclass classification modeling, we have divided the dataset into two parts: train (75%) and test (25%). The performance metrics used were accuracy, specificity, precision, recall, and F1-score. The algorithms used to get the classification results of different models to diagnose antihyperglycemic agents were very accurate. The accuracy of our model in determining these two antihyperglycemic agents was 91-93%. The precision-recall curve showed average precision of 0.91, 0.97, 0.97, and 0.98 for k-nearest neighbors, logistic regression, random forest, and XGB, respectively. The logistic regression, random forest, and XGB had the highest AUC (AUC=0.97) among both biguanides and sulfonylureas groups. The negative predictive values (NPV) for all the models were between 89 and 93%. We introduced a practical web application to help physicians distinguish between these agents. Despite variations in accuracy among the different types of algorithms used, all of them could accurately determine the specific exposure to biguanides and sulfonylureas retrospectively. Machine learning can distinguish antihyperglycemic agents, which may be useful for physicians without any background in medical toxicology. Besides, Our suggested ML-based Web application might help physicians in their diagnosis.
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Affiliation(s)
- Omid Mehrpour
- AI and Health LLC, Tucson, AZ, USA.
- Rocky Mountain Poison & Drug Safety, Denver Health, and Hospital Authority, Denver, CO, USA.
| | - Samaneh Nakhaee
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences (BUMS), Birjand, Iran
| | - Farhad Saeedi
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences (BUMS), Birjand, Iran
- Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran
| | - Bahare Valizade
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences (BUMS), Birjand, Iran
| | - Erfan Lotfi
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences (BUMS), Birjand, Iran
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Abstract
Machine learning methods have been growing in prominence across all areas of medicine. In pathology, recent advances in deep learning (DL) have enabled computational analysis of histological samples, aiding in diagnosis and characterization in multiple disease areas. In cancer, and particularly endocrine cancer, DL approaches have been shown to be useful in tasks ranging from tumor grading to gene expression prediction. This review summarizes the current state of DL research in endocrine cancer histopathology with an emphasis on experimental design, significant findings, and key limitations.
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Affiliation(s)
- Siddhi Ramesh
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center, 5841 South Maryland Avenue, MC 2115, Chicago, IL 60637, USA; The University of Chicago Medicine & Biological Sciences, 5841 South Maryland Avenue, Chicago, IL, USA
| | - James M Dolezal
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center, 5841 South Maryland Avenue, MC 2115, Chicago, IL 60637, USA; The University of Chicago Medicine & Biological Sciences, 5841 South Maryland Avenue, Chicago, IL, USA
| | - Alexander T Pearson
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center, 5841 South Maryland Avenue, MC 2115, Chicago, IL 60637, USA; University of Chicago Comprehensive Cancer Center, Chicago, IL, USA; The University of Chicago Medicine & Biological Sciences, 5841 South Maryland Avenue, Chicago, IL, USA.
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Mehrpour O, Hoyte C, Al Masud A, Biswas A, Schimmel J, Nakhaee S, Nasr MS, Delva-Clark H, Goss F. Deep learning neural network derivation and testing to distinguish acute poisonings. Expert Opin Drug Metab Toxicol 2023; 19:367-380. [PMID: 37395108 DOI: 10.1080/17425255.2023.2232724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 06/30/2023] [Indexed: 07/04/2023]
Abstract
INTRODUCTION Acute poisoning is a significant global health burden, and the causative agent is often unclear. The primary aim of this pilot study was to develop a deep learning algorithm that predicts the most probable agent a poisoned patient was exposed to from a pre-specified list of drugs. RESEARCH DESIGN & METHODS Data were queried from the National Poison Data System (NPDS) from 2014 through 2018 for eight single-agent poisonings (acetaminophen, diphenhydramine, aspirin, calcium channel blockers, sulfonylureas, benzodiazepines, bupropion, and lithium). Two Deep Neural Networks (PyTorch and Keras) designed for multi-class classification tasks were applied. RESULTS There were 201,031 single-agent poisonings included in the analysis. For distinguishing among selected poisonings, PyTorch model had specificity of 97%, accuracy of 83%, precision of 83%, recall of 83%, and a F1-score of 82%. Keras had specificity of 98%, accuracy of 83%, precision of 84%, recall of 83%, and a F1-score of 83%. The best performance was achieved in the diagnosis of single-agent poisoning in diagnosing poisoning by lithium, sulfonylureas, diphenhydramine, calcium channel blockers, then acetaminophen, in PyTorch (F1-score = 99%, 94%, 85%, 83%, and 82%, respectively) and Keras (F1-score = 99%, 94%, 86%, 82%, and 82%, respectively). CONCLUSION Deep neural networks can potentially help in distinguishing the causative agent of acute poisoning. This study used a small list of drugs, with polysubstance ingestions excluded.Reproducible source code and results can be obtained at https://github.com/ashiskb/npds-workspace.git.
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Affiliation(s)
- Omid Mehrpour
- Michigan Poison & Drug Information Center, Wayne State University School of Medicine, Detroit, MI, USA
| | - Christopher Hoyte
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Ashis Biswas
- Department of Computer Science and Engineering, University of Colorado, Denver, CO, USA
| | - Jonathan Schimmel
- Department of Emergency Medicine, Division of Medical Toxicology, Mount Sinai Hospital Icahn School of Medicine, New York, NY, USA
| | - Samaneh Nakhaee
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences (BUMS), Birjand, Iran
| | - Mohammad Sadegh Nasr
- Department of Computer Science and Engineering, The University of Texas at Arlington, Arlington, TX, USA
| | | | - Foster Goss
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora, CO, USA
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Zellner T, Romanek K, Rabe C, Schmoll S, Geith S, Heier EC, Stich R, Burwinkel H, Keicher M, Bani-Harouni D, Navab N, Ahmadi SA, Eyer F. ToxNet: an artificial intelligence designed for decision support for toxin prediction. Clin Toxicol (Phila) 2023; 61:56-63. [PMID: 36373611 DOI: 10.1080/15563650.2022.2144345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Artificial intelligences (AIs) are emerging in the field of medical informatics in many areas. They are mostly used for diagnosis support in medical imaging but have potential uses in many other fields of medicine where large datasets are available. AIM To develop an artificial intelligence (AI) "ToxNet", a machine-learning based computer-aided diagnosis (CADx) system, which aims to predict poisons based on patient's symptoms and metadata from our Poison Control Center (PCC) data. To prove its accuracy and compare it against medical doctors (MDs). METHODS The CADx system was developed and trained using data from 781,278 calls recorded in our PCC database from 2001 to 2019. All cases were mono-intoxications. Patient symptoms and meta-information (e.g., age group, sex, etiology, toxin point of entry, weekday, etc.) were provided. In the pilot phase, the AI was trained on 10 substances, the AI's prediction was compared to naïve matching, literature matching, a multi-layer perceptron (MLP), and the graph attention network (GAT). The trained AI's accuracy was then compared to 10 medical doctors in an individual and in an identical dataset. The dataset was then expanded to 28 substances and the predictions and comparisons repeated. RESULTS In the pilot, the prediction performance in a set of 8995 patients with 10 substances was 0.66 ± 0.01 (F1 micro score). Our CADx system was significantly superior to naïve matching, literature matching, MLP, and GAT (p < 0.005). It outperformed our physicians experienced in clinical toxicology in the individual and identical dataset. In the extended dataset, our CADx system was able to predict the correct toxin in a set of 36,033 patients with 28 substances with an overall performance of 0.27 ± 0.01 (F1 micro score), also significantly superior to naïve matching, literature matching, MLP, and GAT. It also outperformed our MDs. CONCLUSION Our AI trained on a large PCC database works well for poison prediction in these experiments. With further research, it might become a valuable aid for physicians in predicting unknown substances and might be the first step into AI use in PCCs.
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Affiliation(s)
- Tobias Zellner
- Division of Clinical Toxicology, Department of Internal Medicine II, Poison Control Centre Munich, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Katrin Romanek
- Division of Clinical Toxicology, Department of Internal Medicine II, Poison Control Centre Munich, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Christian Rabe
- Division of Clinical Toxicology, Department of Internal Medicine II, Poison Control Centre Munich, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Sabrina Schmoll
- Division of Clinical Toxicology, Department of Internal Medicine II, Poison Control Centre Munich, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Stefanie Geith
- Division of Clinical Toxicology, Department of Internal Medicine II, Poison Control Centre Munich, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Eva-Carina Heier
- Division of Clinical Toxicology, Department of Internal Medicine II, Poison Control Centre Munich, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Raphael Stich
- Division of Clinical Toxicology, Department of Internal Medicine II, Poison Control Centre Munich, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Hendrik Burwinkel
- Computer Aided Medical Procedures, TUM Department of Informatics, Technical University of Munich, Garching, Germany
| | - Matthias Keicher
- Computer Aided Medical Procedures, TUM Department of Informatics, Technical University of Munich, Garching, Germany
| | - David Bani-Harouni
- Computer Aided Medical Procedures, TUM Department of Informatics, Technical University of Munich, Garching, Germany
| | - Nassir Navab
- Computer Aided Medical Procedures, TUM Department of Informatics, Technical University of Munich, Garching, Germany
| | | | - Florian Eyer
- Division of Clinical Toxicology, Department of Internal Medicine II, Poison Control Centre Munich, TUM School of Medicine, Technical University of Munich, Munich, Germany
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Artificial Intelligence in Clinical Toxicology. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Yuan KC, Tsai LW, Lai KS, Teng ST, Lo YS, Peng SJ. Using Transfer Learning Method to Develop an Artificial Intelligence Assisted Triaging for Endotracheal Tube Position on Chest X-ray. Diagnostics (Basel) 2021; 11:diagnostics11101844. [PMID: 34679542 PMCID: PMC8534985 DOI: 10.3390/diagnostics11101844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/21/2021] [Accepted: 09/28/2021] [Indexed: 11/16/2022] Open
Abstract
Endotracheal tubes (ETTs) provide a vital connection between the ventilator and patient; however, improper placement can hinder ventilation efficiency or injure the patient. Chest X-ray (CXR) is the most common approach to confirming ETT placement; however, technicians require considerable expertise in the interpretation of CXRs, and formal reports are often delayed. In this study, we developed an artificial intelligence-based triage system to enable the automated assessment of ETT placement in CXRs. Three intensivists performed a review of 4293 CXRs obtained from 2568 ICU patients. The CXRs were labeled "CORRECT" or "INCORRECT" in accordance with ETT placement. A region of interest (ROI) was also cropped out, including the bilateral head of the clavicle, the carina, and the tip of the ETT. Transfer learning was used to train four pre-trained models (VGG16, INCEPTION_V3, RESNET, and DENSENET169) and two models developed in the current study (VGG16_Tensor Projection Layer and CNN_Tensor Projection Layer) with the aim of differentiating the placement of ETTs. Only VGG16 based on ROI images presented acceptable performance (AUROC = 92%, F1 score = 0.87). The results obtained in this study demonstrate the feasibility of using the transfer learning method in the development of AI models by which to assess the placement of ETTs in CXRs.
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Affiliation(s)
- Kuo-Ching Yuan
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 10675, Taiwan;
- Department of Surgery, DA CHIEN General Hospital, Miaoli 36052, Taiwan
| | - Lung-Wen Tsai
- Department of Medicine Education, Taipei Medical University Hospital, Taipei 110301, Taiwan;
| | - Kevin S. Lai
- Division of Critical Care Medicine, Department of Emergency and Critical Care Medicine, Taipei Medical University Hospital, Taipei 110301, Taiwan; (K.S.L.); (S.-T.T.)
| | - Sing-Teck Teng
- Division of Critical Care Medicine, Department of Emergency and Critical Care Medicine, Taipei Medical University Hospital, Taipei 110301, Taiwan; (K.S.L.); (S.-T.T.)
| | - Yu-Sheng Lo
- Institute of Biomedical Informatics, Taipei Medical University, Taipei 110301, Taiwan
- Correspondence: (Y.-S.L.); (S.-J.P.); Tel.: +886-2-66382736 (Y.-S.L. & S.-J.P.); Fax: +886-2-87320395 (Y.-S.L.); +886-2-27321956 (S.-J.P.)
| | - Syu-Jyun Peng
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei 10675, Taiwan;
- Correspondence: (Y.-S.L.); (S.-J.P.); Tel.: +886-2-66382736 (Y.-S.L. & S.-J.P.); Fax: +886-2-87320395 (Y.-S.L.); +886-2-27321956 (S.-J.P.)
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Porturas T, Taylor RA. Forty years of emergency medicine research: Uncovering research themes and trends through topic modeling. Am J Emerg Med 2020; 45:213-220. [PMID: 33059985 DOI: 10.1016/j.ajem.2020.08.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 10/23/2022] Open
Abstract
STUDY OBJECTIVE Topic identification can facilitate knowledge curation, discover thematic relationships, trends, and predict future direction. We aimed to determine through an unsupervised, machine learning approach to topic modeling the most common research themes in emergency medicine over the last 40 years and summarize their trends and characteristics. METHODS We retrieved the complete reference entries including article abstracts from Ovid for all original research articles from 1980 to 2019 within emergency medicine for six widely-cited journals. Abstracts were processed through a natural language pipeline and analyzed by a latent Dirichlet allocation topic modeling algorithm for unsupervised topic discovery. Topics were further examined through trend analysis, word associations, co-occurrence metrics, and two-dimensional embeddings. RESULTS We retrieved 47,158 articles during the defined time period that were filtered to 20,528 articles for further analysis. Forty topics covering methodologic and clinical areas were discovered. These topics separated into distinct clusters when embedded in two-dimensional space and exhibited consistent patterns of interaction. We observed the greatest increase in popularity in research themes involving risk factors (0.4% to 5.2%), health utilization (1.2% to 5.0%), and ultrasound (0.7% to 3.3%), and a relative decline in research involving basic science (8.9% to 1.1%), cardiac arrest (6.5% to 2.2%), and vitals (6.3% to 1.3%) over the past 40 years. Our data show only very modest growth in mental health and substance abuse research (1.0% to 1.6%), despite ongoing crises. CONCLUSIONS Topic modeling via unsupervised machine learning applied to emergency medicine abstracts discovered coherent topics, trends, and patterns of interaction.
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Affiliation(s)
| | - R Andrew Taylor
- Department of Emergency Medicine, Yale University School of Medicine, United States.
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Verkhivker GM, Agajanian S, Hu G, Tao P. Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning. Front Mol Biosci 2020; 7:136. [PMID: 32733918 PMCID: PMC7363947 DOI: 10.3389/fmolb.2020.00136] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Allosteric regulation is a common mechanism employed by complex biomolecular systems for regulation of activity and adaptability in the cellular environment, serving as an effective molecular tool for cellular communication. As an intrinsic but elusive property, allostery is a ubiquitous phenomenon where binding or disturbing of a distal site in a protein can functionally control its activity and is considered as the "second secret of life." The fundamental biological importance and complexity of these processes require a multi-faceted platform of synergistically integrated approaches for prediction and characterization of allosteric functional states, atomistic reconstruction of allosteric regulatory mechanisms and discovery of allosteric modulators. The unifying theme and overarching goal of allosteric regulation studies in recent years have been integration between emerging experiment and computational approaches and technologies to advance quantitative characterization of allosteric mechanisms in proteins. Despite significant advances, the quantitative characterization and reliable prediction of functional allosteric states, interactions, and mechanisms continue to present highly challenging problems in the field. In this review, we discuss simulation-based multiscale approaches, experiment-informed Markovian models, and network modeling of allostery and information-theoretical approaches that can describe the thermodynamics and hierarchy allosteric states and the molecular basis of allosteric mechanisms. The wealth of structural and functional information along with diversity and complexity of allosteric mechanisms in therapeutically important protein families have provided a well-suited platform for development of data-driven research strategies. Data-centric integration of chemistry, biology and computer science using artificial intelligence technologies has gained a significant momentum and at the forefront of many cross-disciplinary efforts. We discuss new developments in the machine learning field and the emergence of deep learning and deep reinforcement learning applications in modeling of molecular mechanisms and allosteric proteins. The experiment-guided integrated approaches empowered by recent advances in multiscale modeling, network science, and machine learning can lead to more reliable prediction of allosteric regulatory mechanisms and discovery of allosteric modulators for therapeutically important protein targets.
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Affiliation(s)
- Gennady M. Verkhivker
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA, United States
| | - Steve Agajanian
- Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA, United States
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Peng Tao
- Department of Chemistry, Center for Drug Discovery, Design, and Delivery (CD4), Center for Scientific Computation, Southern Methodist University, Dallas, TX, United States
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