![PDF](https://www.biocreative.org/media/store/files/2013/pdf.png)
Proceedings of the BioCreative VII Challenge Evaluation Workshop
![](https://www.biocreative.org/media/store/images/2021/Frontpage.png)
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