Zero-shot Medical Entity Retrieval without Annotation: Learning From Rich Knowledge Graph Semantics (2021.findings-acl)
Copied to clipboard
| Challenge: | Current approaches to medical entity retrieval generalize poorly to unseen sub-specialties . zero-shot retrieval is challenging due to the high degree of ambiguity and variability in medical corpora . |
| Approach: | They propose a set of learning tasks designed to train efficient zero-shot entity retrieval models. |
| Outcome: | The proposed architecture outperforms common zero-shot benchmarks with 7% to 30% higher recall across multiple major medical ontologies. |
Similar Papers
AutoMIR: Effective Zero-Shot Medical Information Retrieval without Relevance Labels (2025.findings-emnlp)
Copied to clipboard
| Challenge: | Effective zero-shot dense retrieval in the medical domain remains difficult due to the scarcity of relevance-labeled data. |
| Approach: | They propose a framework that leverages large language models to generate hypothetical documents . they also propose 'CMIRB' to provide a rigorous evaluation suite . |
| Outcome: | The proposed framework outperforms HyDE in retrieval accuracy and generalization . it leverages large language models to generate hypothetical documents conditioned on a query . |
Entity Decomposition with Filtering: A Zero-Shot Clinical Named Entity Recognition Framework (2025.naacl-long)
Copied to clipboard
| Challenge: | Recent studies have demonstrated that large language models (LLMs) can perform in named entity recognition tasks. |
| Approach: | They propose a framework for clinical named entity recognition that decomposes the entity recognition task into several retrievals of sub-types and then filters them. |
| Outcome: | The proposed framework improves on the clinical named entity recognition task. |
Scalable Zero-shot Entity Linking with Dense Entity Retrieval (2020.emnlp-main)
Copied to clipboard
| Challenge: | Existing methods for entity linking use manually curated mention tables and incoming Wikipedia link popularity. |
| Approach: | They propose a BERT-based entity linking model with a bi-encoder that embeds the mention context and the entity descriptions and then re-ranked the candidate with . they also evaluate the accuracy-speed trade-off inherent to large pre-trained models. |
| Outcome: | The proposed model is state-of-the-art on recent zero-shot benchmarks and established non-zero-shot evaluations. |
Virtual Knowledge Graph Construction for Zero-Shot Domain-Specific Document Retrieval (2022.coling-1)
Copied to clipboard
| Challenge: | Domain-specific documents cover terminologies and specialized knowledge. |
| Approach: | They propose a domain-specific document retrieval method that embeds a document into a graph of entities and their relations into . they compare the unsupervised method with previous approaches and use it to compute relevance between queries and documents. |
| Outcome: | The proposed method outperforms baselines and fully-supervised bi-encoders in a zero-shot setting and outperformed bi-supervised approaches. |
Zero-Shot Entailment Learning for Ontology-Based Biomedical Annotation Without Explicit Mentions (2025.coling-main)
Copied to clipboard
Rumana Ferdous Munne, Noriki Nishida, Shanshan Liu, Narumi Tokunaga, Yuki Yamagata, Kouji Kozaki, Yuji Matsumoto
| Challenge: | Automated biomedical annotation presents significant challenges when entities are not explicitly mentioned in the text. |
| Approach: | They propose an entailment-based zero-shot text classification approach to annotate biomedical text passages using the Homeostasis Imbalance Process (HOIP) ontology. |
| Outcome: | The proposed method performs well when processes are not explicitly mentioned . it is time-consuming and expensive to annotate biomedical texts with a specific ontology . |
Towards a Versatile Medical-Annotation Guideline Feasible Without Heavy Medical Knowledge: Starting From Critical Lung Diseases (2020.lrec-1)
Copied to clipboard
| Challenge: | Current annotation policies for medical corpora are not standardized across clinical texts of different types. |
| Approach: | They propose to annotate medical records of various types using a named entity recognition (NER) task. |
| Outcome: | The proposed annotation scheme is applicable to large-scale clinical NLP projects. |
Incorporating medical knowledge in BERT for clinical relation extraction (2021.emnlp-main)
Copied to clipboard
| Challenge: | Pre-trained language models (PLMs) are used for diverse NLP tasks such as Information Extraction, Sentiment Analysis and Question/Answering. |
| Approach: | They propose to add medical knowledge to pre-trained language models to facilitate clinical relation extraction using a large text corpus. |
| Outcome: | The proposed model outperforms the state-of-the-art systems on the benchmark i2b2/VA 2010 clinical relation extraction dataset. |
Leveraging Type Descriptions for Zero-shot Named Entity Recognition and Classification (2021.acl-long)
Copied to clipboard
| Challenge: | Named entity recognition and classification (NERC) tasks require annotated data for the target classes during training. |
| Approach: | They propose a novel approach that leverages the fact that textual descriptions for many entity classes occur naturally. |
| Outcome: | The proposed approach outperforms baselines adapted from machine reading comprehension and zero-shot text classification. |
Knowledge-Rich Self-Supervision for Biomedical Entity Linking (2022.findings-emnlp)
Copied to clipboard
Sheng Zhang, Hao Cheng, Shikhar Vashishth, Cliff Wong, Jinfeng Xiao, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, Hoifung Poon
| Challenge: | Entity linking is challenging in high-value domains with myriad entities . standard classification approaches suffer from the annotation bottleneck . |
| Approach: | They propose a self-supervised approach to learn domain knowledge for biomedical entity linking . it generates self-reported mention examples on unlabeled text and trains contextual encoder . |
| Outcome: | The proposed method outperforms existing methods by 20 points in accuracy on biomedical datasets. |
Large language models are few-shot clinical information extractors (2022.emnlp-main)
Copied to clipboard
| Challenge: | a long-running goal of clinical NLP is the extraction of important variables trapped in clinical notes. |
| Approach: | They propose to use large language models to tackle diverse clinical extraction tasks . they propose to reannote existing CASI datasets to compare their models with clinical text. |
| Outcome: | The proposed models outperform existing models on few-shot clinical information extraction tasks. |