yusuke1997/dblp-id-title huggingface dataset:
External Evaluation of Event Extraction Classifiers for Automatic Pathway Curation: An extended study of the mTOR pathway
Recognizing Nested Named Entities in GENIA corpus
REAL: A Retrieval-Augmented Entity Linking Approach for Biomedical Concept Recognition
Structuring Operative Notes using Active Learning
Document-level Clinical Entity and Relation extraction via Knowledge Base-Guided Generation
Complex Biological Event Extraction from Full Text using Signatures of Linguistic and Semantic Features
Integrating Co-occurrence Statistics with Information Extraction for Robust Retrieval of Protein Interactions from Medline
Earlier Identification of Epilepsy Surgery Candidates Using Natural Language Processing
SNP2Vec: Scalable Self-Supervised Pre-Training for Genome-Wide Association Study
A Pragmatic Approach to Summary Extraction in Clinical Trials
Pre-training data selection for biomedical domain adaptation using journal impact metrics
Generalizing an Approximate Subgraph Matching-based System to Extract Events in Molecular Biology and Cancer Genetics
Bootstrapping and Evaluating Named Entity Recognition in the Biomedical Domain
Trigger Word Detection and Thematic Role Identification via BERT and Multitask Learning
Scaling up WSD with Automatically Generated Examples
Deep Learning for Punctuation Restoration in Medical Reports
Comparing Encoder-Only and Encoder-Decoder Transformers for Relation Extraction from Biomedical Texts: An Empirical Study on Ten Benchmark Datasets
Roux-lette at "Discharge Me!": Reducing EHR Chart Burden with a Simple, Scalable, Clinician-Driven AI Approach
Generative Content Models for Structural Analysis of Medical Abstracts
PubTermVariants: biomedical term variants and their use for PubMed search
Translating Electronic Health Record Notes from English to Spanish: A Preliminary Study
Proactive Learning for Named Entity Recognition
BEEDS: Large-Scale Biomedical Event Extraction using Distant Supervision and Question Answering
Natural Language Processing Methods for Enhancing Geographic Metadata for Phylogeography of Zoonotic Viruses
PharmaCoNER: Pharmacological Substances, Compounds and proteins Named Entity Recognition track
Restoring the intended structure of Hungarian ophthalmology documents
BioNLP Shared Task 2011 - Bacteria Gene Interactions and Renaming
BioELECTRA: Pretrained Biomedical text Encoder using Discriminators
Classifying the reported ability in clinical mobility descriptions
Using Hedges to Enhance a Disease Outbreak Report Text Mining System
Generating Patient Problem Lists from the ShARe Corpus using SNOMED CT/SNOMED CT CORE Problem List
WBI at MEDIQA 2021: Summarizing Consumer Health Questions with Generative Transformers
Continuous Predictive Modeling of Clinical Notes and ICD Codes in Patient Health Records
Overview of the BioLaySumm 2024 Shared Task on the Lay Summarization of Biomedical Research Articles
Bio-Medical Entity Extraction using Support Vector Machines
Detecting Health Related Discussions in Everyday Telephone Conversations for Studying Medical Events in the Lives of Older Adults
Towards Generalizable Methods for Automating Risk Score Calculation
Incorporating Lexical Knowledge into Biomedical NE Recognition
BEL Networks Derived from Qualitative Translations of BioNLP Shared Task Annotations
Evaluating Feature Extraction Methods for Knowledge-based Biomedical Word Sense Disambiguation
The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, BioNLP@ACL 2023, Toronto, Canada, 13 July 2023
Evaluation of ChatGPT on Biomedical Tasks: A Zero-Shot Comparison with Fine-Tuned Generative Transformers
The Role of Information Extraction in the Design of a Document Triage Application for Biocuration
Overview of BioNLP Shared Task 2013
e-Health CSIRO at RadSum23: Adapting a Chest X-Ray Report Generator to Multimodal Radiology Report Summarisation
Clinical Abbreviation Disambiguation Using Neural Word Embeddings
MLBMIKABR at "Discharge Me!": Concept Based Clinical Text Description Generation
IxaMed at PharmacoNER Challenge 2019
Tagging Funding Agencies and Grants in Scientific Articles using Sequential Learning Models
Clinical Case Reports for NLP
ANU-CSIRO at MEDIQA 2019: Question Answering Using Deep Contextual Knowledge
Augmenting Reddit Posts to Determine Wellness Dimensions impacting Mental Health
Evaluating Large Language Models for Predicting Protein Behavior under Radiation Exposure and Disease Conditions
Exploring Drug Switching in Patients: A Deep Learning-based Approach to Extract Drug Changes and Reasons from Social Media
Toward Automated Early Sepsis Alerting: Identifying Infection Patients from Nursing Notes
A distantly supervised dataset for automated data extraction from diagnostic studies
Ctyun AI at BioLaySumm: Enhancing Lay Summaries of Biomedical Articles Through Large Language Models and Data Augmentation
From Pathways to Biomolecular Events: Opportunities and Challenges
Determining causal and non-causal relationships in biomedical text by classifying verbs using a Naive Bayesian Classifier
Assessing the Feasibility of an Automated Suggestion System for Communicating Critical Findings from Chest Radiology Reports to Referring Physicians
Proceedings of BioNLP Shared Task 2011 Workshop, Portland, Oregon, USA, June 24, 2011
Parsing Natural Language Queries for Life Science Knowledge
Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011
Paragraph Retrieval for Enhanced Question Answering in Clinical Documents
Unsupervised Document Classification with Informed Topic Models
Information Extraction from Patients' Free Form Documentation
Memory-aligned Knowledge Graph for Clinically Accurate Radiology Image Report Generation
Bacteria Biotope Relation Extraction via Lexical Chains and Dependency Graphs
Open (Clinical) LLMs are Sensitive to Instruction Phrasings
NLNDE: Enhancing Neural Sequence Taggers with Attention and Noisy Channel for Robust Pharmacological Entity Detection
Fast and simple semantic class assignment for biomedical text
MiDRED: An Annotated Corpus for Microbiome Knowledge Base Construction
Extracting Time Expressions from Clinical Text
CRAFT Shared Tasks 2019 Overview - Integrated Structure, Semantics, and Coreference
Double Layered Learning for Biological Event Extraction from Text
Is That the Right Dose? Investigating Generative Language Model Performance on Veterinary Prescription Text Analysis
Convolutional neural networks for chemical-disease relation extraction are improved with character-based word embeddings
Complex Event Extraction using DRUM
IITP at MEDIQA 2019: Systems Report for Natural Language Inference, Question Entailment and Question Answering
Intra-Template Entity Compatibility based Slot-Filling for Clinical Trial Information Extraction
Clustering Semantic Spaces of Suicide Notes and Newsgroups Articles
EPFL-MAKE at "Discharge Me!": An LLM System for Automatically Generating Discharge Summaries of Clinical Electronic Health Record
Evaluating distributed word representations for capturing semantics of biomedical concepts
Zero-shot Temporal Relation Extraction with ChatGPT
From indexing the biomedical literature to coding clinical text: experience with MTI and machine learning approaches
Stacked Generalization for Medical Concept Extraction from Clinical Notes
Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, BioNLP-OST@EMNLP-IJNCLP 2019, Hong Kong, China, November 4, 2019
Data Augmentation for Biomedical Factoid Question Answering
Disambiguation of Biomedical Abbreviations
Quantitative Data on Referring Expressions in Biomedical Abstracts
Sieg at MEDIQA 2019: Multi-task Neural Ensemble for Biomedical Inference and Entailment
High-precision biological event extraction with a concept recognizer
Resolving Elliptical Compounds in German Medical Text
From Graphs to Events: A Subgraph Matching Approach for Information Extraction from Biomedical Text
Overview of the Regulatory Network of Plant Seed Development (SeeDev) Task at the BioNLP Shared Task 2016
CSIRO Data61 Team at BioLaySumm Task 1: Lay Summarisation of Biomedical Research Articles Using Generative Models
Biomedical Document Classification with Literature Graph Representations of Bibliographies and Entities
IKM_Lab at BioLaySumm Task 1: Longformer-based Prompt Tuning for Biomedical Lay Summary Generation
Applying the TARSQI Toolkit to Augment Text Mining of EHRs
XAI for Better Exploitation of Text in Medical Decision Support
Benchmark and Best Practices for Biomedical Knowledge Graph Embeddings
Combining Compositionality and Pagerank for the Identification of Semantic Relations between Biomedical Words
Reconstruction of Semantic Relationships from Their Projections in Biomolecular Domain
QUB-Cirdan at "Discharge Me!": Zero shot discharge letter generation by open-source LLM
UTSA-NLP at RadSum23: Multi-modal Retrieval-Based Chest X-Ray Report Summarization
A Framework for Developing and Evaluating Word Embeddings of Drug-named Entity
Learning from the Experience of Doctors: Automated Diagnosis of Appendicitis Based on Clinical Notes
Classifying Gene Sentences in Biomedical Literature by Combining High-Precision Gene Identifiers
Exploring Label Dependency in Active Learning for Phenotype Mapping
Adaptation of POS Tagging for Multiple BioMedical Domains
Zero-Shot Aspect-Based Scientific Document Summarization using Self-Supervised Pre-training
Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings
Automatic Extraction of Disease Risk Factors from Medical Publications
A Hybrid approach for biomedical event extraction
Ontology alignment in the biomedical domain using entity definitions and context
Towards Automatic Generation of Gene Summary
Unlocking Medical Ontologies for Non-Ontology Experts
Surf at MEDIQA 2019: Improving Performance of Natural Language Inference in the Clinical Domain by Adopting Pre-trained Language Model
From Protein-Protein Interaction to Molecular Event Extraction
Utility Preservation of Clinical Text After De-Identification
Two-stage Federated Phenotyping and Patient Representation Learning
Using the Argumentative Structure of Scientific Literature to Improve Information Access
Building Timelines from Narrative Clinical Records: Initial Results Based-on Deep Natural Language Understanding
The Difficulties of Taxonomic Name Extraction and a Solution
Stacking With Auxiliary Features for Entity Linking in the Medical Domain
Incorporating Medical Knowledge to Transformer-based Language Models for Medical Dialogue Generation
Exploring Partial Knowledge Base Inference in Biomedical Entity Linking
BioCite: A Deep Learning-based Citation Linkage Framework for Biomedical Research Articles
Domain Adaptation of SRL Systems for Biological Processes
GenCompareSum: a hybrid unsupervised summarization method using salience
Using Argumentation to Retrieve Articles with Similar Citations from MEDLINE
SINAI at BioLaySumm: Self-Play Fine-Tuning of Large Language Models for Biomedical Lay Summarisation
Improving Biomedical Analogical Retrieval with Embedding of Structural Dependencies
Identification of Patients with Acute Lung Injury from Free-Text Chest X-Ray Reports
Model Combination for Event Extraction in BioNLP 2011
Identification of Mentions and Relations between Bacteria and Biotope from PubMed Abstracts
DISTANT-CTO: A Zero Cost, Distantly Supervised Approach to Improve Low-Resource Entity Extraction Using Clinical Trials Literature
Bootstrapping Biomedical Ontologies for Scientific Text using NELL
An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining
Low Resource ICD Coding of Hospital Discharge Summaries
Domain-specific or Uncertainty-aware models: Does it really make a difference for biomedical text classification?
Bridging the Gap between Domain-Oriented and Linguistically-Oriented Semantics
Two-Phase Biomedical NE Recognition based on SVMs
Overview of the RadSum23 Shared Task on Multi-modal and Multi-anatomical Radiology Report Summarization
Medical Entity Recognition: A Comparaison of Semantic and Statistical Methods
Incorporating Syntactic Dependency Information towards Improved Coding of Lengthy Medical Concepts in Clinical Reports
Event Extraction as Dependency Parsing for BioNLP 2011
UETrice at MEDIQA 2021: A Prosper-thy-neighbour Extractive Multi-document Summarization Model
Temporal Expressions in Swedish Medical Text - A Pilot Study
Building a Corpus for Biomedical Relation Extraction of Species Mentions
Improving Correlation with Human Judgments by Integrating Semantic Similarity with Second-Order Vectors
Unsupervised Domain Adaptation for Clinical Negation Detection
SimSem: Fast Approximate String Matching in Relation to Semantic Category Disambiguation
BioNLP Shared Task 2013 - An overview of the Genic Regulation Network Task
Using Kybots for Extracting Events in Biomedical Texts
Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013
Exploring Graph Structure for Detection of Reliability Zones within Synonym Resources: Experiment with the Gene Ontology
Automatic classification of doctor-patient questions for a virtual patient record query task
A Machine Learning Approach to Clinical Terms Normalization
Applying deep learning on electronic health records in Swedish to predict healthcare-associated infections
Proceedings of the 19th SIGBioMed Workshop on Biomedical Language Processing, BioNLP 2020, Online, July 9, 2020
Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction
MedExQA: Medical Question Answering Benchmark with Multiple Explanations
e-Health CSIRO at RRG24: Entropy-Augmented Self-Critical Sequence Training for Radiology Report Generation
Creating Ontology-annotated Corpora from Wikipedia for Medical Named-entity Recognition
LasigeBioTM at MEDIQA 2019: Biomedical Question Answering using Bidirectional Transformers and Named Entity Recognition
Coding Structures and Actions with the COSTA Scheme in Medical Conversations
Transfer Learning for Causal Sentence Detection
Combining multiple evidence for gene symbol disambiguation
Unsupervised Learning of the Morpho-Semantic Relationship in MEDLINE
Proceedings of the 15th Workshop on Biomedical Natural Language Processing, BioNLP@ACL 2016, Berlin, Germany, August 12, 2016
Extracting Drug-Drug Interactions with Attention CNNs
Automated Disease Normalization with Low Rank Approximations
Towards Automatic Curation of Antibiotic Resistance Genes via Statement Extraction from Scientific Papers: A Benchmark Dataset and Models
NLM at MEDIQA 2021: Transfer Learning-based Approaches for Consumer Question and Multi-Answer Summarization
A Multi-strategy Query Processing Approach for Biomedical Question Answering: USTB_PRIR at BioASQ 2017 Task 5B
Analysing Representations of Memory Impairment in a Clinical Notes Classification Model
Intervention extraction in preclinical animal studies of Alzheimer's Disease: Enhancing regex performance with language model-based filtering
An Unsupervised Method for Extracting Domain-specific Affixes in Biological Literature
Automatic extraction of data deposition statements: where do the research results go?
EVEX in ST'13: Application of a large-scale text mining resource to event extraction and network construction
BIOptimus: Pre-training an Optimal Biomedical Language Model with Curriculum Learning for Named Entity Recognition
Domain Adaptation of Coreference Resolution for Radiology Reports
A preliminary study on automatic identification of patient smoking status in unstructured electronic health records
An extended dependency graph for relation extraction in biomedical texts
Detecting Entity Relations as a Supporting Task for Bio-Molecular Event Extraction
VERSE: Event and Relation Extraction in the BioNLP 2016 Shared Task
Exploring Two Biomedical Text Genres for Disease Recognition
Extracting Epilepsy Patient Data with Llama 2
Proceedings of the BioNLP 2018 workshop, Melbourne, Australia, July 19, 2018
Annotation of pain and anesthesia events for surgery-related processes and outcomes extraction
Overview of BioNLP'09 Shared Task on Event Extraction
KU_ai at MEDIQA 2019: Domain-specific Pre-training and Transfer Learning for Medical NLI
Lexical Characteristics Analysis of Chinese Clinical Documents
ConText: An Algorithm for Identifying Contextual Features from Clinical Text
CID at RRG24: Attempting in a Conditionally Initiated Decoding of Radiology Report Generation with Clinical Entities
Team: PULSAR at ProbSum 2023: PULSAR: Pre-training with Extracted Healthcare Terms for Summarising Patients' Problems and Data Augmentation with Black-box Large Language Models
Evidence Inference 2.0: More Data, Better Models
Chunking Clinical Text Containing Non-Canonical Language
Can Character Embeddings Improve Cause-of-Death Classification for Verbal Autopsy Narratives?
Rapid Adaptation of POS Tagging for Domain Specific Uses
Data Augmentation for Rare Symptoms in Vaccine Side-Effect Detection
MDC at BioLaySumm Task 1: Evaluating GPT Models for Biomedical Lay Summarization
Unsupervised Linguistically-Driven Reliable Dependency Parses Detection and Self-Training for Adaptation to the Biomedical Domain
Overview of the MEDIQA 2019 Shared Task on Textual Inference, Question Entailment and Question Answering
Improved Semantic Representation for Domain-Specific Entities
IRISA participation to BioNLP-ST13: lazy-learning and information retrieval for information extraction tasks
End-to-end Biomedical Entity Linking with Span-based Dictionary Matching
A Fine-grained citation graph for biomedical academic papers: the finding-citation graph
ICDBigBird: A Contextual Embedding Model for ICD Code Classification
Doctor XAvIer: Explainable Diagnosis on Physician-Patient Dialogues and XAI Evaluation
CoMAGD: Annotation of Gene-Depression Relations
BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes
Automatic Diagnosis Coding of Radiology Reports: A Comparison of Deep Learning and Conventional Classification Methods
Entity-Enriched Neural Models for Clinical Question Answering
Automatically Restructuring Practice Guidelines using the GEM DTD
Towards Visual Dialog for Radiology
DeepGeneMD: A Joint Deep Learning Model for Extracting Gene Mutation-Disease Knowledge from PubMed Literature
Extraction of Lactation Frames from Drug Labels and LactMed
Using Bottleneck Adapters to Identify Cancer in Clinical Notes under Low-Resource Constraints
Named Entity Recognition for Cancer Immunology Research Using Distant Supervision
A sequence-to-sequence approach for document-level relation extraction
Semi-supervised anaphora resolution in biomedical texts
Protein Word Detection using Text Segmentation Techniques
Proceedings of the 2011 Workshop on Biomedical Natural Language Processing, BioNLP@ACL, Portland, Oregon, USA, June 23-24, 2011
Assessing the performance of Olelo, a real-time biomedical question answering application
iHealth-Chile-3&2 at RRG24: Template Based Report Generation
Extracting Complex Biological Events with Rich Graph-Based Feature Sets
Adaptive Information Extraction for Complex Biomedical Tasks
HGP-NLP at BioLaySumm: Leveraging LoRA for Lay Summarization of Biomedical Research Articles using Seq2Seq Transformers
BiCAL: Bi-directional Contrastive Active Learning for Clinical Report Generation
Performance and limitations of the linguistically motivated Cocoa/Peaberry system in a broad biological domain
MAIRA at RRG24: A specialised large multimodal model for radiology report generation
BLAR: Biomedical Local Acronym Resolver
PANLP at MEDIQA 2019: Pre-trained Language Models, Transfer Learning and Knowledge Distillation
Embedding Transfer for Low-Resource Medical Named Entity Recognition: A Case Study on Patient Mobility
Coreference Resolution for Structured Drug Product Labels
ONYX: A System for the Semantic Analysis of Clinical Text
DISTANT: Distantly Supervised Entity Span Detection and Classification
An improved corpus of disease mentions in PubMed citations
Saama Research at MEDIQA 2019: Pre-trained BioBERT with Attention Visualisation for Medical Natural Language Inference
Biomedical Event Extraction using Abstract Meaning Representation
VSP at PharmaCoNER 2019: Recognition of Pharmacological Substances, Compounds and Proteins with Recurrent Neural Networks in Spanish Clinical Cases
Efficient Biomedical Entity Linking: Clinical Text Standardization with Low-Resource Techniques
Event Extraction in pieces: Tackling the partial event identification problem on unseen corpora
Low Resource Causal Event Detection from Biomedical Literature
This before That: Causal Precedence in the Biomedical Domain
Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011
SnapToGrid: From Statistical to Interpretable Models for Biomedical Information Extraction
Corpus-Driven Terminology Development: Populating Swedish SNOMED CT with Synonyms Extracted from Electronic Health Records
Parallels between Linguistics and Biology
Analysis of Link Grammar on Biomedical Dependency Corpus Targeted at Protein-Protein Interactions
Analyzing text in search of bio-molecular events: a high-precision machine learning framework
A Deep Learning-Based System for PharmaCoNER
Towards BERT-based Automatic ICD Coding: Limitations and Opportunities
Proceedings of the 18th BioNLP Workshop and Shared Task, BioNLP@ACL 2019, Florence, Italy, August 1, 2019
Finding small molecule and protein pairs in scientific literature using a bootstrapping method
Decision Style in a Clinical Reasoning Corpus
Term Generalization and Synonym Resolution for Biological Abstracts: Using the Gene Ontology for Subcellular Localization Prediction
Extracting Biomedical Events and Modifications Using Subgraph Matching with Noisy Training Data
Proceedings of BioNLP, Baltimore, Maryland, USA, BioNLP@ACL 2014, June 27-28, 2014
A Data-driven Approach for Noise Reduction in Distantly Supervised Biomedical Relation Extraction
A Comparative Study of Syntactic Parsers for Event Extraction
Evaluating and Improving Automatic Speech Recognition using Severity
Extraction of Named Entities from Tables in Gene Mutation Literature
Sub-word information in pre-trained biomedical word representations: evaluation and hyper-parameter optimization
RNN Embeddings for Identifying Difficult to Understand Medical Words
Domain Adaptation for Disease Phrase Matching with Adversarial Networks
BioNoculars: Extracting Protein-Protein Interactions from Biomedical Text
Automatic Glossary of Clinical Terminology: a Large-Scale Dictionary of Biomedical Definitions Generated from Ontological Knowledge
Role-Preserving Redaction of Medical Records to Enable Ontology-Driven Processing
Detecting Dementia through Retrospective Analysis of Routine Blog Posts by Bloggers with Dementia
Extensive Error Analysis and a Learning-Based Evaluation of Medical Entity Recognition Systems to Approximate User Experience
Keyphrases Extraction from User-Generated Contents in Healthcare Domain Using Long Short-Term Memory Networks
Grading the Quality of Medical Evidence
IIT-KGP at MEDIQA 2019: Recognizing Question Entailment using Sci-BERT stacked with a Gradient Boosting Classifier
Bacteria Biotope at BioNLP Open Shared Tasks 2019
How You Say It Matters: Measuring the Impact of Verbal Disfluency Tags on Automated Dementia Detection
Extracting drug indications and adverse drug reactions from Spanish health social media
ARS_NITK at MEDIQA 2019: Analysing Various Methods for Natural Language Inference, Recognising Question Entailment and Medical Question Answering System
Character based String Kernels for Bio-Entity Relation Detection
Effect of small sample size on text categorization with support vector machines
Molecular event extraction from Link Grammar parse trees
Extracting Clinical Relationships from Patient Narratives
Biological, translational, and clinical language processing, BioNLP@ACL 2007, Prague, Czech Republic, June 29, 2007
ELiRF-VRAIN at BioNLP Task 1B: Radiology Report Summarization
Extracting Biological Pathway Models From NLP Event Representations
New Resources and Perspectives for Biomedical Event Extraction
SAFFRON: tranSfer leArning For Food-disease RelatiOn extractioN
Not all links are equal: Exploiting Dependency Types for the Extraction of Protein-Protein Interactions from Text