# Biomedical Question Answering: A Survey of Approaches and Challenges

arXiv: https://arxiv.org/abs/2102.05281 · HTML: https://mlsanity.com/paper/2102.05281/

## Key facts

- Cited by 46 papers in the map (data through 14 Oct 2026).
- Builds on 96 of its 246 references that are in the map.
- First posted on arXiv 10 Feb 2021.

## Builds on (most cited first, 30 of 96)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Very Deep Convolutional Networks for Large-Scale Image Recognition](https://mlsanity.com/paper/1409.1556/) (2014)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [Model-Agnostic Meta-Learning for Fast Adaptation of Deep Networks](https://mlsanity.com/paper/1703.03400/) (2017)
- [Neural Machine Translation by Jointly Learning to Align and Translate](https://mlsanity.com/paper/1409.0473/) (2014)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [SQuAD: 100,000+ Questions for Machine Comprehension of Text](https://mlsanity.com/paper/1606.05250/) (2016)
- [HotpotQA: A Dataset for Diverse, Explainable Multi-hop Question Answering](https://mlsanity.com/paper/1809.09600/) (2018)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [TriviaQA: A Large Scale Distantly Supervised Challenge Dataset for Reading Comprehension](https://mlsanity.com/paper/1705.03551/) (2017)
- [A Broad-Coverage Challenge Corpus for Sentence Understanding through Inference](https://mlsanity.com/paper/1704.05426/) (2017)
- [Deep contextualized word representations](https://mlsanity.com/paper/1802.05365/) (2018)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [A large annotated corpus for learning natural language inference](https://mlsanity.com/paper/1508.05326/) (2015)
- [Know What You Don't Know: Unanswerable Questions for SQuAD](https://mlsanity.com/paper/1806.03822/) (2018)
- [LXMERT: Learning Cross-Modality Encoder Representations from Transformers](https://mlsanity.com/paper/1908.07490/) (2019)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [VisualBERT: A Simple and Performant Baseline for Vision and Language](https://mlsanity.com/paper/1908.03557/) (2019)
- [Get To The Point: Summarization with Pointer-Generator Networks](https://mlsanity.com/paper/1704.04368/) (2017)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Teaching Machines to Read and Comprehend](https://mlsanity.com/paper/1506.03340/) (2015)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Attention is not Explanation](https://mlsanity.com/paper/1902.10186/) (2019)
- [RACE: Large-scale ReAding Comprehension Dataset From Examinations](https://mlsanity.com/paper/1704.04683/) (2017)
- [Reading Wikipedia to Answer Open-Domain Questions](https://mlsanity.com/paper/1704.00051/) (2017)

## Built on by (most cited first, 30 of 46)

- [MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval](https://mlsanity.com/paper/2307.00589/) (2023)
- [A Survey of Large Language Models in Medicine: Progress, Application, and Challenge](https://mlsanity.com/paper/2311.05112/) (2023)
- [Opportunities and Challenges for ChatGPT and Large Language Models in Biomedicine and Health](https://mlsanity.com/paper/2306.10070/) (2023)
- [GeneGPT: Augmenting Large Language Models with Domain Tools for Improved Access to Biomedical Information](https://mlsanity.com/paper/2304.09667/) (2023)
- [BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model](https://mlsanity.com/paper/2204.03905/) (2022)
- [Better to Ask in English: Cross-Lingual Evaluation of Large Language Models for Healthcare Queries](https://mlsanity.com/paper/2310.13132/) (2023)
- [Benchmarking large language models for biomedical natural language processing applications and recommendations](https://mlsanity.com/paper/2305.16326/) (2023)
- [Matching Patients to Clinical Trials with Large Language Models](https://mlsanity.com/paper/2307.15051/) (2023)
- [Improving Retrieval-Augmented Generation in Medicine with Iterative Follow-up Questions](https://mlsanity.com/paper/2408.00727/) (2024)
- [MedicalAgentsBench for Complex Medical Reasoning: Comparing Internalized Reasoning Models versus Externalized Agent-based Frameworks](https://mlsanity.com/paper/2503.07459/) (2025)
- [HealthFC: Verifying Health Claims with Evidence-Based Medical Fact-Checking](https://mlsanity.com/paper/2309.08503/) (2023)
- [RAMM: Retrieval-augmented Biomedical Visual Question Answering with Multi-modal Pre-training](https://mlsanity.com/paper/2303.00534/) (2023)
- [BioInstruct: Instruction Tuning of Large Language Models for Biomedical Natural Language Processing](https://mlsanity.com/paper/2310.19975/) (2023)
- [UNIQORN: Unified Question Answering over RDF Knowledge Graphs and Natural Language Text](https://mlsanity.com/paper/2108.08614/) (2021)
- [PubMed and Beyond: Biomedical Literature Search in the Age of Artificial Intelligence](https://mlsanity.com/paper/2307.09683/) (2023)
- [A Survey on Medical Document Summarization](https://mlsanity.com/paper/2212.01669/) (2022)
- [Progress and Opportunities of Foundation Models in Bioinformatics](https://mlsanity.com/paper/2402.04286/) (2024)
- [DORIS-MAE: Scientific Document Retrieval using Multi-level Aspect-based Queries](https://mlsanity.com/paper/2310.04678/) (2023)
- [BIOS: An Algorithmically Generated Biomedical Knowledge Graph](https://mlsanity.com/paper/2203.09975/) (2022)
- [Product Question Answering in E-Commerce: A Survey](https://mlsanity.com/paper/2302.08092/) (2023)
- [BioMamba: Domain-Adaptive Biomedical Language Models](https://mlsanity.com/paper/2408.02600/) (2024)
- [An Accurate Unsupervised Method for Joint Entity Alignment and Dangling Entity Detection](https://mlsanity.com/paper/2203.05147/) (2022)
- [Structured Outputs Enable General-Purpose LLMs to be Medical Experts](https://mlsanity.com/paper/2503.03194/) (2025)
- [Large-Scale Knowledge Synthesis and Complex Information Retrieval from Biomedical Documents](https://mlsanity.com/paper/2302.06854/) (2023)
- [Memorization in Large Language Models in Medicine: Prevalence, Characteristics, and Implications](https://mlsanity.com/paper/2509.08604/) (2025)
- [Large Language Models are In-context Teachers for Knowledge Reasoning](https://mlsanity.com/paper/2311.06985/) (2023)
- [BioMol-MQA: A Multi-Modal Question Answering Dataset For LLM Reasoning Over Bio-Molecular Interactions](https://mlsanity.com/paper/2506.05766/) (2025)
- [Development of an Extractive Clinical Question Answering Dataset with Multi-Answer and Multi-Focus Questions](https://mlsanity.com/paper/2201.02517/) (2022)
- [BioADAPT-MRC: Adversarial Learning-based Domain Adaptation Improves Biomedical Machine Reading Comprehension Task](https://mlsanity.com/paper/2202.13174/) (2022)
- [SpaceQA: Answering Questions about the Design of Space Missions and Space Craft Concepts](https://mlsanity.com/paper/2210.03422/) (2022)

## Abstract (arXiv)

Automatic Question Answering (QA) has been successfully applied in various domains such as search engines and chatbots. Biomedical QA (BQA), as an emerging QA task, enables innovative applications to effectively perceive, access and understand complex biomedical knowledge. There have been tremendous developments of BQA in the past two decades, which we classify into 5 distinctive approaches: classic, information retrieval, machine reading comprehension, knowledge base and question entailment approaches. In this survey, we introduce available datasets and representative methods of each BQA approach in detail. Despite the developments, BQA systems are still immature and rarely used in real-life settings. We identify and characterize several key challenges in BQA that might lead to this issue, and discuss some potential future directions to explore.