Models:
Joseph Gordon
joseph-gordon/
DRUDIS-D-23-00233R1
0
Downloads: 1
[ab519f]: / data / table_3.tsv

Download this file

# Article DOI business objective NLP methods metrics datasets # protocols # criteria protocol source auxiliary datasets ground truth preprocessing shallow ML methods neural models knowledge bases main contribution
1 Study of Pre-trained Language Models for Named Entity Recognition in Clinical Trial Eligibility Criteria from Multiple Corpora 10.1109/ICHI52183.2021.00095 CT parsing NER PRF Covance, ELilE, Chia 1700.0 internal, ClinicalTrials.gov normalization BERT, SpanBERT, BlueBERT, BioBERT, PubMedBERT, SciBERT evaluation
2 Accuracy of an Artificial Intelligence System for Cancer Clinical Trial Eligibility Screening: Retrospective Pilot Study 10.2196/27767 patient CT matching not specified accuracy, sensitivity, specificity, PPV, NPV not specified 4.0 internal, ClinicalTrials.gov manual evaluation
3 Extending the Query Language of a Data Warehouse for Patient Recruitment 10.3233/978-1-61499-808-2-152 patient CT matching IR recall internal EHR manual regex, negation detection evaluation
4 An Evaluation of Pretrained BERT Models for Comparing Semantic Similarity Across Unstructured Clinical Trial Texts 10.3233/SHTI210848 CT similarity STS similarity not specified 689.0 internal, ClinicalTrials.gov manual cosine similarity BERT, BioBERT, BlueBERT, ClinicalBioBERT, SciBERT, PubMedBERT, CODER evaluation
5 Automated classification of eligibility criteria in clinical trials to facilitate patient-trial matching for specific patient populations 10.1093/jamia/ocw176 patient CT matching classification PRF, AUC not specified 3462.0 ClinicalTrials.gov manual TF-IDF, term normalization, negation detection SVM method
6 A Unified Machine Reading Comprehension Framework for Cohort Selection 10.1109/JBHI.2021.3095478 CT design QA F1 i2b2/n2c2 26.0 manual normalization, keyword filtering BERT, RoBERTa, BioBERT, word2vec, Glove, FastText, BiLSTM, BiDAF method
7 ASCOT: A text mining-based web-service for efficient search and assisted creation of clinical trials 10.1186/1472-6947-12-S1-S3 CT design NER not specified keyword filtering, term normalization evaluation
8 Cohort selection for clinical trials using deep learning models 10.1093/jamia/ocz139 n2c2 challenge not specified F1 i2b2/n2c2 13.0 word2vec, CNN, GRU, FCFF method
9 EliIE: An open-source information extraction system for clinical trial eligibility criteria 10.1093/jamia/ocx019 CT parsing NER, RE, normalization F1, accuracy not specified 230.0 ClinicalTrials.gov manual normalization, negation detection SVM, CRF protocol
10 Classifying Eligibility Criteria in Clinical Trials Using Active Deep Learning 10.1109/ICMLA.2018.00052 patient CT matching classification error rate not specified 9762.0 209441.0 NCI method
11 Protocol Feasibility Workflow Using an Automated Multi-country Patient Cohort System 10.3233/978-1-61499-432-9-985 patient CT matching not specified not specified not specified method
12 Assessing clinical trial eligibility with logic expression queries 10.1016/j.datak.2007.07.005 patient CT matching IR, normalization PRF not specified 100.0 1545.0 ClinicalTrials.gov manual normalization, custom transformations method
13 Improving the efficiency of clinical trial recruitment using electronic health record data, natural language processing, and machine learning 10.1002/art.41108 patient CT matching NER sensitivity, PPV, custom internal 15.0 manual RF, logistic regression UMLS method
14 Automatic trial eligibility surveillance based on unstructured clinical data 10.1016/j.ijmedinf.2019.05.018 patient CT matching NER, classification, EL recall, precision, AUC, MAP internal 3.0 24.0 ClinicalTrials.gov EHR manual normalization, term normalization, custom transformations, regex SVM, cosine similarity, custom rules method
15 Information Extraction from Free Text in Clinical Trials with Knowledge-based Distant Supervision 10.1109/COMPSAC.2019.00158 CT parsing normalization accuracy, recall not specified 100.0 386.0 ClinicalTrials.gov UMLS, Wikipedia, OHDSI method
16 ETACTS: A method for dynamically filtering clinical trial search results 10.1016/j.jbi.2013.07.014 patient CT matching STS custom internal 141291.0 ClinicalTrials.gov synthetic EHR POS, keyword filtering, term normalization jaccard similarity, custom rules evaluation
17 A practical method for transforming free-text eligibility criteria into computable criteria 10.1016/j.jbi.2010.09.007 CT parsing normalization custom not specified ClinicalTrials.gov manual keyword filtering, custom transformations dependency parsing UMLS method
18 Evaluation of an artificial intelligence clinical trial matching system in Australian lung cancer patients 10.1093/jamiaopen/ooaa002 patient CT matching not specified accuracy, precision, recall, PPV, NPV internal 10.0 11467.0 internal, ClinicalTrials.gov EHR manual evaluation
19 Increasing the efficiency of trial-patient matching: automated clinical trial eligibility Pre-screening for pediatric oncology patients 10.1186/s12911-015-0149-3 patient CT matching IR precision, recall, NPV, specificity internal 55.0 ClinicalTrials.gov EHR manual keyword filtering, negation detection, regex, sentence segmentation custom rules UMLS, SNOMED, RxNORM method
20 An eligibility criteria query language for heterogeneous data warehouses 10.3414/ME13-02-0027 patient CT matching IR, EL custom internal 17.0 208.0 CCR, HL7 RIM method
21 DeepEnroll: Patient-Trial Matching with Deep Embedding and Entailment Prediction 10.1145/3366423.3380181 patient CT matching NLI F1, AUC IQVIA 794.0 12445.0 ClinicalTrials.gov IQVIA, Synthea manual numerical normalization, BOW MLP, ClinicalBERT method
22 Improving Clinical Trial Participant Prescreening With Artificial Intelligence (AI): A Comparison of the Results of AI-Assisted vs Standard Methods in 3 Oncology Trials 10.1177/2168479018815454 patient CT matching NLI custom, precision not specified 3.0 CBCC manual OCR Mendel.ai SNOMED, ICD method
23 ExaCT: automatic extraction of clinical trial characteristics from journal publications 10.1186/1472-6947-10-56 CT parsing IR precision, recall not specified 182.0 PubMed manual BOW, keyword filtering, normalization, regex, sentence segmentation SVM evaluation
24 Building a specialized lexicon for breast cancer clinical trial subject eligibility analysis 10.1177/1460458221989392 patient CT matching IR, EL custom NCI dictionary, breastcancer.org, emedicinehealth.org 378.0 ClinicalTrials.gov NCI dictionary, ACS website, breastcancer.org TF-IDF SNOMED protocol
25 An OMOP CDM-Based Relational Database of Clinical Research Eligibility Criteria 10.3233/978-1-61499-830-3-950 CT parsing NER, normalization, RE PRF not specified 1587.0 ClinicalTrials.gov manual POS, negation detection, term normalization, sentence segmentation SVM SNOMED, ICD method
26 An Ensemble Learning Strategy for Eligibility Criteria Text Classification for Clinical Trial Recruitment: Algorithm Development and Validation 10.2196/17832 CT parsing classification accuracy, PRF not specified 38341.0 internal manual regex, normalization GBM BERT, BERNIE, XLNet, RoBERTa method
27 Chia, a large annotated corpus of clinical trial eligibility criteria 10.1038/s41597-020-00620-0 dataset building not specified PRF, Cohen kappa Chia 1000.0 12409.0 ClinicalTrials.gov manual dataset
28 Cohort selection for clinical trials using multiple instance learning 10.1016/j.jbi.2020.103438 patient CT matching classification F1 i2b2/n2c2 13.0 benchmark dataset term normalization, regex, negation detection, TF-IDF SVM, KNN, custom rules method
29 Learning Eligibility in Cancer Clinical Trials Using Deep Neural Networks 10.3390/app8071206 patient CT matching classification PRF, Cohen kappa not specified 49201.0 6186572.0 ClinicalTrials.gov protocol text BOW, custom transformations, normalization, sentence segmentation SVM, KNN word2vec, CNN method
30 Valx: A System for Extracting and Structuring Numeric Lab Test Comparison Statements from Text 10.3414/ME15-01-0112 CT parsing IR, normalization PRF not specified 4383.0 ClinicalTrials.gov manual normalization, regex, custom transformations UMLS evaluation
31 EMR2vec: Bridging the gap between patient data and clinical trial 10.1016/j.cie.2021.107236 patient CT matching classification, NER, STS, EL PRF, p@k i2b2/n2c2 31500.0 ClinicalTrials.gov manual term normalization, negation detection SVM, CRF, custom rules CNN, LSTM, BioBERT, word2vec, BiLSTM, BiLSTM-CRF, BioBERT-CRF method
32 How the clinical research community responded to the COVID-19 pandemic: an analysis of the COVID-19 clinical studies in ClinicalTrials.gov 10.1093/jamiaopen/ooab032 CT parsing IR precision, recall not specified 3765.0 ClinicalTrials.gov manual term normalization, TF-IDF, PCA k-means, custom rules MeSH method
33 DQueST: dynamic questionnaire for search of clinical trials 10.1093/jamia/ocz121 patient CT matching NER, IR, EL custom internal 252330.0 ClinicalTrials.gov manual BOW, negation detection, numerical normalization, custom transformations, term normalization, sentence segmentation custom rules, clustering, CRF OHDSI evaluation
34 Conflict discovery and analysis for clinical trials 10.1145/3079452.3079494 CT parsing IR custom not specified 134.0 ClinicalTrials.gov normalization custom rules UMLS method
35 COVID-19 trial graph: a linked graph for COVID-19 clinical trials 10.1093/jamia/ocab078 CT design IR, normalization precision, recall not specified 3392.0 ClinicalTrials.gov manual normalization SVM, RF, GBM, logistic regression GNN, t-SNE, node2vec OMOP CDM dataset
36 Identifying the status of genetic lesions in cancer clinical trial documents using machine learning 10.1186/1471-2164-13-S8-S21 CT parsing NER, IR, EL accuracy internal 250.0 1143.0 NCI manual POS, negation detection, keyword filtering SVM method
37 Parsing clinical trial eligibility criteria for cohort query by a multi-input multi-output sequence labeling model 10.1101/2021.11.18.21266533 patient CT matching NER, IR PRF, AUC not specified 13.0 ClinicalTrials.gov manual POS, normalization BERT, BioRoBERTa evaluation
38 Transformer-Based Named Entity Recognition for Parsing Clinical Trial Eligibility Criteria 10.1145/3459930.3469560 CT parsing NER PRF not specified 4314.0 ClinicalTrials.gov MIMIC-III manual BERT, RoBERTa, ELECTRA, ALBERT method
39 Cohort Selection for Clinical Trials From Longitudinal Patient Records: Text Mining Approach 10.2196/15980 patient CT matching STS F1 not specified 13.0 n2c2 benchmark dataset custom transformations, normalization, BOW, keyword filtering, sentence segmentation SVM, logistic regression, NBC, GTB method
40 Medical knowledge infused convolutional neural networks for cohort selection in clinical trials 10.1093/jamia/ocz128 patient CT matching RL PRF not specified 13.0 n2c2 benchmark dataset term normalization, normalization, keyword filtering, sentence segmentation CNN, word2vec method
41 Semantic categorization of Chinese eligibility criteria in clinical trials using machine learning methods 10.1186/s12911-021-01487-w patient CT matching RL PRF not specified 272.0 ChiCTR manual normalization, custom transformations logistic regression, NBC, KNN, SVM CNN, RNN, FastText, BERT, ERNIE UMLS method
42 Building an OMOP common data model-compliant annotated corpus for COVID-19 clinical trials 10.1016/j.jbi.2021.103790 CT parsing NER, IR Cohen kappa not specified 700.0 11710.0 ClinicalTrials.gov manual regex, normalization OMOP CDM dataset
43 Improving Disease Named Entity Recognition for Clinical Trial Matching 10.1109/BIBM47256.2019.8983421 CT parsing NER PRF not specified 7500.0 NCBI, TREC BiLSTM-CRF, ELMO, Glove UMLS, SNOMED, MEDICS method
44 Analysis of eligibility criteria representation in industry-standard clinical trial protocols 10.1016/j.jbi.2013.06.001 CT parsing normalization, RL, STS custom not specified 32.0 internal, ClinicalTrials.gov manual keyword filtering, term normalization, custom transformations, sentence segmentation cosine similarity, custom rules UMLS method
45 Syntactic and Semantic Knowledge-Aware Paraphrase Detection for Clinical Data 10.1007/978-981-16-2937-2_13 patient CT matching STS, classification PRF MSRP, TREC 2018 3160.0 ClinicalTrials.gov MSRP manual char-level embedding ClinicalBERT, word2vec, CliNER, FCFF, LSTM UMLS, DrugBank, CTD method
46 Criteria2Query: A natural language interface to clinical databases for cohort definition 10.1093/jamia/ocy178 CT design NER PRF, accuracy not specified 407.0 ClinicalTrials.gov manual regex, normalization, custom transformations, negation detection, sentence segmentation CRF UMLS evaluation
47 Textual inference for eligibility criteria resolution in clinical trials 10.1016/j.jbi.2015.09.008 patient CT matching NLI F1 i2b2/n2c2, internal 5054.0 4.0 ClinicalTrials.gov EHR manual keyword filtering, normalization, custom transformations, sentence segmentation custom rules UMLS method
48 Inferring appropriate eligibility criteria in clinical trial protocols without labeled data 10.1145/2390068.2390074 CT design STS, classification, topic modeling similarity not specified 44203.0 462459.0 ClinicalTrials.gov CT.gov structured data BOW, keyword filtering, normalization LDA, logistic regression, custom rules, cosine similarity method
49 Formulating queries for assessing clinical trial eligibility 10.1007/11765448_8 patient CT matching IR custom internal 25000.0 ClinicalTrials.gov EHR manual custom transformations, regex, sentence segmentation custom rules SNOMED method
50 Numerical Eligibility Criteria in Clinical Protocols: Annotation, Automatic Detection and Interpretation 10.1007/978-3-319-59758-4_22 patient CT matching NER Cohen kappa not specified 211438.0 2000000.0 ClinicalTrials.gov manual custom transformations CRF method
51 Automated learning of domain taxonomies from text using background knowledge 10.1016/j.jbi.2016.09.002 dataset building IR, RE PRF, silhouette, purity 455773.0 ClinicalTrials.gov manual term normalization, normalization, sentence segmentation jaccard similarity, HAC UMLS, SNOMED, DBPedia, MEDLINE method
52 Feasibility of Feature-based Indexing, Clustering, and Search of Clinical Trials 10.3414/ME12-01-0092 CT parsing clustering Cohen kappa not specified 80.0 ClinicalTrials.gov manual term normalization, custom transformations, sentence segmentation HAC, custom rules UMLS method
53 Predictive modeling of clinical trial terminations using feature engineering and embedding learning 10.1038/s41598-021-82840-x CT design RL accuracy, F1, AUC not specified 68999.0 ClinicalTrials.gov custom transformations RF, XGB, logistic regression MLP method
54 Automated clinical trial eligibility prescreening: increasing the efficiency of patient identification for clinical trials in the emergency department 10.1136/amiajnl-2014-002887 patient CT matching IR F1, MAP, custom not specified 13.0 not specified manual normalization, BOW, negation detection, TF-IDF, custom transformations, sentence segmentation custom rules UMLS, SNOMED, RxNORM method
55 Supporting Patient Screening to Identify Suitable Clinical Trials 10.3233/978-1-61499-432-9-823 patient CT matching NER custom not specified internal custom rules SNOMED, LOINC method
56 Attention-Based LSTM Network for COVID-19 Clinical Trial Parsing 10.1109/BigData50022.2020.9378451 CT design NER PRF CTP 2998.0 27352.0 ClinicalTrials.gov manual term normalization custom rules BiLSTM, word2vec MeSH method
57 Patterns for conflict identification in clinical trial eligibility criteria 10.1109/HealthCom.2016.7749519 patient CT matching IR custom not specified 56.0 1588.0 ClinicalTrials.gov normalization, term normalization, sentence segmentation custom rules UMLS method
58 Artificial Intelligence Tool for Optimizing Eligibility Screening for Clinical Trials in a Large Community Cancer Center 10.1200/CCI.19.00079 patient CT matching not specified accuracy, sensitivity, specificity, PPV, NPV not specified 4.0 218.0 ClinicalTrials.gov manual POS, negation detection, normalization evaluation
59 Clinical Trial Information Extraction with BERT 10.1109/ICHI52183.2021.00092 CT design NER PRF CTP, Criteria2Query 10.0 45483.0 ClinicalTrials.gov benchmark dataset normalization CRF, BiLSTM, BERT, BioBERT, BlueBERT, ClinicalBERT method
60 A knowledge base of clinical trial eligibility criteria 10.1016/j.jbi.2021.103771 CT parsing NER, IR, RE custom not specified 352110.0 3647567.0 ClinicalTrials.gov manual OMOP CDM, SNOMED, RxNORM dataset
61 Classification And Extraction Of Medical Clinical Trial Screening Standard Texts Based On Bi-Lstm And Attention Mechanism 10.1088/1755-1315/632/5/052088 patient CT matching classification PRF not specified not specified word2vec, BiLSTM method
62 Understanding Common Key Indicators Of Successful And Unsuccessful Cancer Drug Trials Using A Contrast Mining Framework On Clinicaltrials.Gov 10.1016/j.jbi.2023.104321 CT design RL support, growth, PRF not specified 18304.0 ClinicalTrials.gov CT.gov structured data term normalization RF, logistic regression UMLS, DrugBank method
63 A Comparative Study Of Pre-Trained Language Models For Named Entity Recognition In Clinical Trial Eligibility Criteria From Multiple Corpora 10.1186/s12911-022-01967-7 CT parsing NER PRF Covance, ELilE, Chia 1700.0 internal, ClinicalTrials.gov benchmark dataset normalization BERT, SpanBERT, PubMedBERT, BioBERT, BlueBERT, SciBERT method
64 Improving Clinical Trial Design Using Interpretable Machine Learning Based Prediction Of Early Trial Termination 10.1038/s41598-023-27416-7 CT design NER accuracy, F1, AUC Chia 112647.0 ClinicalTrials.gov CT.gov structured data custom transformations logistic regression, RF, XGB, SHAP, custom rules dataset
65 Combining Human And Machine Intelligence For Clinical Trial Eligibility Querying 10.1093/jamia/ocac051 CT design NER, EL accuracy, PRF internal 1015.0 ClinicalTrials.gov EHR manual POS, normalization, numerical normalization, regex BERT, PubMedBERT method
66 A Scalable Ai Approach For Clinical Trial Cohort Optimization 10.1007/978-3-030-93733-1_36 CT design NER Optum database 125.0 3572.0 ClinicalTrials.gov EHR keyword filtering CT-BERT method
67 The Leaf Clinical Trials Corpus: A New Resource For Query Generation From Clinical Trial Eligibility Criteria 10.1038/s41597-022-01521-0 patient CT matching NER, RE F1 Chia, LCT 1006.0 ClinicalTrials.gov manual BiLSTM-CRF, BERT, PubMedBERT, SciBERT dataset
68 Piloting An Automated Clinical Trial Eligibility Surveillance And Provider Alert System Based On Artificial Intelligence And Standard Data Models 10.1186/s12874-023-01916-6 patient CT matching IR, NER PRF MUSC warehouse 5.0 EHR manual regex SVM, custom rules, cosine similarity method
69 Hint: Hierarchical Interaction Network For Clinical-Trial-Outcome Predictions 10.1016/j.patter.2022.100445 CT classification RL AUC, F1 internal 12500.0 ClinicalTrials.gov drug-related datasets CT.gov structured data GNN, CNN, ClinicalBERT DrugBank, ICD method
70 Predicting Publication Of Clinical Trials Using Structured And Unstructured Data: Model Development And Validation Study 10.2196/38859 CT classification RL AUC, F1 75000.0 ClinicalTrials.gov MEDLINE TF-IDF RF FCFF, BERT, SciBERT MEDLINE method
71 Growth In Eligibility Criteria Content And Failure To Accrue Among National Cancer Institute (Nci)-Affiliated Clinical Trials 10.1002/cam4.5276 CT design IR, NER, RL AUC, R2 not specified 1197.0 ClinicalTrials.gov CT.gov structured data normalization, custom transformations custom rules, XGB, logistic regression SciSpaCy method
72 Utilizing Large Language Models For Enhanced Clinical Trial Matching: A Study On Automation In Patient Screening 10.7759/cureus.60044 patient CT matching classification, RAG accuracy, recall, precision, F1, specificity i2b2/n2c2 13.0 n2c2 benchmark dataset GPT-3.5-turbo, GPT-4, ada-002 method
73 Autocriteria: A Generalizable Clinical Trial Eligibility Criteria Extraction System Powered By Large Language Models 10.1093/jamia/ocad218 CT parsing IR precision, recall, F1, accuracy internal 432.0 ClinicalTrials.gov manual regex GPT-4, Davinci-003 method
74 Automatic Assessment Of Patient Eligibility By Utilizing Nlp And Rule-Based Analysis 10.1109/EMBC40787.2023.10340494 patient CT matching classification, STS precision, recall internal 1.0 direct protocol EHR manual keyword filtering, term normalization, regex, custom transformations custom rules, cosine similarity BioSentVec ICD method
75 Characterisation Of Digital Therapeutic Clinical Trials: A Systematic Review With Natural Language Processing 10.1016/S2589-7500(23)00244-3 CT analysis topic modeling accuracy internal 449.0 ClinicalTrials.gov manual sentence segmentation BERTopic, SciSpaCy method
76 Sociotechnical Feasibility Of Natural Language Processing-Driven Tools In Clinical Trial Eligibility Prescreening For Alzheimer'S Disease And Related Dementias 10.1093/jamia/ocae032 patient CT matching IR ICC, custom internal 2.0 direct protocol EHR manual evaluation
77 A Self-Learning Resource-Efficient Re-Ranking Method For Clinical Trials Search 10.1145/3583780.3615174 patient CT matching classification, ranking P@10, RR, NDCG@10 TREC 2021, TREC 2022 375580.0 ClinicalTrials.gov benchmark dataset custom rules, BM25 SciBERT, monoBERT method
78 Automated Matching Of Patients To Clinical Trials: A Patient-Centric Natural Language Processing Approach For Pediatric Leukemia 10.1200/CCI.23.00009 patient CT matching classification accuracy, precision, recall, time internal 216.0 5251.0 ClinicalTrials.gov synthetic EHR manual regex, custom transformations, sentence segmentation SVM, custom rules FastText method
79 Effective Matching Of Patients To Clinical Trials Using Entity Extraction And Neural Re-Ranking 10.1016/j.jbi.2023.104444 patient CT matching NER, classification, ranking P@10, RR, NDCG@10, NDCG@5 TREC 2021, TREC 2022 375580.0 ClinicalTrials.gov benchmark dataset custom transformations, negation detection, keyword filtering, sentence segmentation BM25 monoBERT, traditionalRR, SciSpaCy, medSpaCy, BERT, BioBERT, ClinicalBERT
80 Distilling Large Language Models For Matching Patients To Clinical Trials 10.1093/jamia/ocae073 patient CT matching classification, ranking NDCG@10, P@10, AUROC, precision, recall, F1, custom SIGIR, TREC 2021, TREC 2022, internal 23280.0 ClinicalTrials.gov GPT-created GPT-3.5-turbo, GPT-4, LLAMA-2-7B, LLAMA-2-13B, LLAMA-2-70B dataset, evaluation
81 Named Entity Recognition and Normalization for Alzheimer's Disease Eligibility Criteria 10.1109/ICHI57859.2023.00100 CT parsing NER, normalization precision, recall, F1 internal 1508.0 ClinicalTrials.gov manual custom transformations custom rules, CRF SapBERT UMLS method
82 Criteria2Query 3.0: Leveraging Generative Large Language Models For Clinical Trial Eligibility Query Generation 10.1016/j.jbi.2024.104649 CT parsing NER, normalization precision, recall, F1 not specified 20.0 ClinicalTrials.gov manual GPT-4, GPT-3.5 OMOP CDM method
83 Treement: Interpretable Patient-Trial Matching Via Personalized Dynamic Tree-Based Memory Network 10.1145/3584371.3612998 patient CT matching RL, classification, normalization F1, accuracy internal 590.0 12445.0 ClinicalTrials.gov EHR manual normalization beam search MLP, Tree-MemNN, ClinicalBERT, Transformer Encoder USC method