Full version of Proceedings

Proceedings of the BioCreative VII Challenge Evaluation Workshop

ISBN: 978-0-578-32368-8

Table of Contents: BC VII - Workshop Proceedings

• Preface Proceedings of the BioCreative VII Challenge Evaluation Workshop, 3
• BioCreative VII Committees Proceedings of the BioCreative VII Challenge Evaluation Workshop, 4
• BioCreative VII Scientific Program Proceedings of the BioCreative VII Challenge Evaluation Workshop, 5

Keynotes and Panels

• Keynote: All of Us Research Program: Improving Health Through Technology, Huge Cohorts and Precision Medicine Joshua Denny, M.D., M.S. Chief Executive Officer of the All of Us Research Program, NIH Proceedings of the BioCreative VII Challenge Evaluation Workshop, 9
• Panel: Challenges in mining adverse drug reactions Proceedings of the BioCreative VII Challenge Evaluation Workshop, 9
  • Dr. Martin Krallinger (Chair)
  • CDR Monica Muñoz, FDA CDER
  • Prof. Özlem Uzuner, George Mason University
  • Dr. Raul Rodriguez-Esteban, Roche Pharmaceutics
  • Prof. Graciela Gonzalez-Hernandez, U Pennsylvania Medical School

Track 1 DrugProt:Text mining drug/chemical-protein interactions

• Overview of DrugProt BioCreative VII track: quality evaluation and large scale text mining of drug-gene/protein relations Miranda-Escalada et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 11
• Humboldt @ DrugProt: Chemical-Protein Relation Extraction with Pretrained Transformers and Entity Descriptions Weber et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 22
• Extracting Drug-Protein Interaction using an Ensemble of Biomedical Pre-trained Language Models through Sequence Labeling and Text Classification Techniques Ling Luo Luo et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 26
• Using Knowledge Base to Refine Data Augmentation for Biomedical Relation Extraction Yoon et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 31
• UTHealth@BioCreativeVII: Domain-specific Transformer Models for Drug-Protein Relation Extraction Das et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 36
• Does constituency analysis enhance domain-specific pre-trained BERT models for relation extraction? Tang et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 40
• CU-UD: text-mining drug and chemical-protein interactions with ensembles of BERT-based models Karabulut et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 45
• TTI-COIN at BioCreative VII Track 1 Iinuma et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 49
• Text Mining Drug-Protein Interactions using an Ensemble of BERT, Sentence BERT and T5 models Sui et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 54
• Text Mining Drug/Chemical-Protein Interactions using an Ensemble of BERT and T5 Based Models Adams et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 59
• Using Knowledge-Based Pretrained Language Model for Mining Drug and Chemical-Protein Interactions Li et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 63
• A Multi-Task Transfer Learning-based method for Extracting Drug-Protein Interactions Ed-drissiya El-allaly et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 67
• BioCreative VII-Track 1: A BERT-based System for Relation Extraction in Biomedical Text Mahendran et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 71
• Chemical–protein relation extraction in PubMed abstracts using BERT and neural networks Antunes et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 76
• Dependencies for Drug-Prot Relation Extraction CLaC at BioCreative VII Track 1 Bagherzadeh et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 80
• Catalytic DS at BioCreative VII: DrugProt Track Mehay et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 84
• Drug-protein relation extraction using ensemble of transformer-based language models Copara et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 89
• lasigeBioTM at BioCreative VII Track 1: Text mining drug and chemical-protein interactions using biomedical ontologies Sousa et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 94
• Identifying Drug/chemical-protein Interactions in Biomedical Literature using the BERT-based Ensemble Learning Approach for the BioCreative 2021 DrugProt Track Chang et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 98
• R-BERT-CNN: Drug-target interactions extraction from biomedical literature. BioCreative Challenge VII Track 1 submission Aldahdooh et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 102

Track 2 NLM-Chem Track: Full text Chemical Identification and Indexing in PubMed articles

• Overview of the NLM-Chem BioCreative VII track: Full-text Chemical Identification and Indexing in PubMed articles Leaman et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 108
• The chemical corpus of the NLM-Chem BioCreative VII track: Full-text Chemical Identification and Indexing in PubMed articles. Islamaj et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 114
• Chemical detection and indexing in PubMed full text articles using deep learning and rule-based methods Almeida et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 119
• Rule-based Enhancement of Stanza Chemical NER Mercer et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 124
• Recognizing Chemical Entity in Biomedical Literature using a BERT-based Ensemble Learning Methods for the BioCreative 2021 NLM-Chem Track Chiu et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 127
• A BERT-Based Hybrid System for Chemical Identification and Indexing in Full-Text Articles Erdengasileng et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 130
• Combining dictionary- and rule-based approximate entity linking with tuned BioBERT Mobasher et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 135
• Improving Tagging Consistency and Entity Coverage for Chemical Identification in Full-text Articles Kim et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 140
• Fine-tuning transformers for automatic chemical entity identification in PubMed articles Bevan et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 144
• Chemical Identification and Indexing in PubMed Articles via BERT and Text-to-Text Based Approaches Adams et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 148
• Chemical entity recognition and MeSH normalization in PubMed full-text literature using BioBERT López-Úbeda et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 152
• TTI-COIN at BioCreative VII Track 2 Tsujimura et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 156

Track 3 Automatic extraction of medication names in tweets

• BioCreative VII – Task 3: Automatic Extraction of Medication Names in Tweets Weissenbacher et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 163
• NCU-IISR/AS-GIS: Detecting Medication Names in Imbalanced Twitter Data with Pretrained Extractive QA Model and Data-Centric Approach Zhang et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 168
• BCH-NLP at BioCreative VII Track 3 – medications detection in tweets using transformer networks and multi-task learning Xu et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 173
• Automatic Extraction of Medication Names in Tweets as Named Entity Recognition Anderson et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 177
• PubMedBERT-based Classifier with Data Augmentation Strategy for Detecting Medication Mentions in Tweets Han et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 180
• Extraction of Medication Names from Twitter Using Augmentation and an Ensemble of Language Models Kulev et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 185
• Boosting Transformers using Background Knowledge, or how to detect Drug Mentions in Social Media using Limited Data Roller et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 189
• A lexicon-based approach to predicting pregnancy-related medication mentions by Twitter users Piccolo. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 194
• Medication Mention Extraction in Tweets using DistilBERT with Bootstrapping Han et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 198
• An Enhanced Approach to Identify and Extract Medication Mentions in Tweets via Weak Supervision Tekumalla et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 201
• Extraction of Medication Names from Tweets CLaC at BioCreative VII Track 3 Bagherzadeh et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 206
• Drug Mention Recognition in Twitter Posts Using a Deep Learning Approach Silva et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 210
• Creating Domain Specific Embeddings to Work with Imbalanced Datasets in Automatic Extraction of Medication Names in Tweets Zavala et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 214
• Data Augmentation for BERT in the Medication Extraction Task of BioCreative VII Lee et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 218
• An ensemble approach for classification and extraction of drug mentions in Tweets Hernandez et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 221

Track 4 COVID-19 text mining tool interactive demo

• Overview of the COVID-19 Text Mining Tool Interactive Demo Track Chatr-Aryamontri et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 227
• Semantic Search Engine preVIEW COVID-19 - Evaluation in the BioCreative VII IAT Track Darms et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 233
• TopEx: Topic Exploration of COVID-19 Corpora - Results from the Biocreative VII Challenge Track 4 Olex et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 238
• Interpretable Visualization of Scientific Hypotheses in Literature-based Discovery Tyagin et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 243
• A self-updating causal model of COVID-19 mechanisms built from the scientific literature Gyori et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 249
• BioKDE: a Deep Learning Powered Search Engine and Biomedical Knowledge Discovery Platform Chung et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 254
• The COVID-19 Therapeutic Information Browser Korves et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 260

Track 5 LitCovid track Multi-label topic classification for COVID-19 literature annotation

• Overview of the BioCreative VII LitCovid Track: Multi-label Topic Classification for COVID-19 Literature Annotation Chen et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 266
• Team Bioformer at BioCreative VII LitCovid Track: Multic-label Topic Classification for COVID-19 Literature with a Compact BERT Model Fang et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 272
• Team BJUT-BJFU at BioCreative VII LitCovid Track: A Deep Learning based Method for Multi-label Topic Classification in COVID-19 Literature Xu et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 275
• CLaC at BioCreative VII LitCovid Track: Independent Modules for Multi-label Classification of Covid Articles Bagherzadeh et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 278
• Team CUNI-NU at BioCreative VII LitCovid Track: Multi-label Topical Classification of Scientific Articles using SPECTER Embeddings with Dual Attention and Label-Wise Attention Network Bhatnagar et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 283
• Team DonutNLP at BioCreativeVII LitCovid Track: Multilabel Topic Classification for COVID-19 Literature Annotation using the BERT-based Ensemble Learning Approach Lin et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 289
• Team DUT914 at BioCreative VII LitCovid Track: A BioBERT-based feature enhancement approach Tang et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 292
• Team E8@IJS at BioCreative VII LitCovid Track 5: Multi-label classification of COVID-19-related articles with an autoML approach Tavchioski et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 295
• Team Elsevier Health Data Science at BioCreative VII LitCovid Track: Fine-Tuning Transformer Models for COVID-19 Literature Annotation Sugumar et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 300
• Team FSU2021 at BioCreative VII LitCovid Track: BERT-based models using different strategies for topic annotation of COVID-19 literature Tian et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 302
• Team ITTC at BioCreative VII LitCovid Track 5: combining pre-trained and bag-of-words models Otmakhova et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 306
• KnowLab at BioCreative VII Track 5 LitCovid: Ensemble of deep learning models from diverse sources for COVID-19 literature classification Dong et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 310
• Team LIA/LS2N at BioCreative VII LitCovid Track: Multi-label Document Classification for COVID-19 Literature using Keyword Based Enhancement and Few-Shot Learning Labrak et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 314
• LRL_NC at BioCreative VII LitCovid Track: Multi-Label Classification of COVID-19 Literature using ML-Based Approaches Tandon et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 319
• Team Opscidia at BioCreative VII LitCovid Track: BERT-based bagging-stacking for multi-topic classification Rakotoson et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 323
• Team PolyU-CBSNLP at BioCreative-VII LitCovid Track: Ensemble Learning for COVID-19 Multilabel Classification Gu et al.Proceedings of the BioCreative VII Challenge Evaluation Workshop, 326
• RobertNLP at the BioCreative VII - LitCovid track: Neural Document Classification Using SciBERT Pujari et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 332
• SINAI at BioCreative VII LitCovid Track: Corpus augmentation for COVID-19 literature multi-label classification Chizhikova et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 336
• Team TCSR at BioCreative VII LitCovid Track: Automated topic prediction of LitCovid using BioBERT Saipradeep et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 341

Posters

• Claim Detection in Biomedical Twitter Posts as a Prerequisite for Fact-Checking Wührl et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 345
• Visual Exploration of Randomized Clinical Trials for COVID-19 Correa Dias et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 347
• COVID-SEE: The Scientific Evidence Explorer for COVID-19 Related Research Verspoor et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 351
• Long Covid: A Comprehensive Collection of Articles on Post-COVID Conditions Leaman et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 353
• Automated topic prediction of LitCovid using BioBERT Saipradeep et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 356
• A SURVEY OF RELATION EXTRACTION TECHNIQUES USING HYBRID CLASSICAL AND STATE OF THE ART METHODS Kara et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 358
• A COVID-19 Knowledge Graph for Therapeutic Discovery from Semantic Integration of Literature and Databases Ross et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 360
• Current Challenges in Optimizing the Capture of all Publications Pertaining to a Protein Family and its Members Reed et al. Proceedings of the BioCreative VII Challenge Evaluation Workshop, 361