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Register a new userCan Language Models be Biomedical Knowledge Bases?
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Added by
Mujeen Sung
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Pre-trained language models (LMs) have become ubiquitous in solving various natural language processing (NLP) tasks. There has been increasing interest in what knowledge these LMs contain and how we can extract that knowledge, treating LMs as knowledge bases (KBs). While there has been much work on probing LMs in the general domain, there has been little attention to whether these powerful LMs can be used as domain-specific KBs. To this end, we create the BioLAMA benchmark, which is comprised of 49K biomedical factual knowledge triples for probing biomedical LMs. We find that biomedical LMs with recently proposed probing methods can achieve up to 18.51% Acc@5 on retrieving biomedical knowledge. Although this seems promising given the task difficulty, our detailed analyses reveal that most predictions are highly correlated with prompt templates without any subjects, hence producing similar results on each relation and hindering their capabilities to be used as domain-specific KBs. We hope that BioLAMA can serve as a challenging benchmark for biomedical factual probing.
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Pretrained language models have shown success in many natural language processing tasks. Many works explore incorporating knowledge into language models. In the biomedical domain, experts have taken decades of effort on building large-scale knowledge bases. For example, the Unified Medical Language System (UMLS) contains millions of entities with their synonyms and defines hundreds of relations among entities. Leveraging this knowledge can benefit a variety of downstream tasks such as named entity recognition and relation extraction. To this end, we propose KeBioLM, a biomedical pretrained language model that explicitly leverages knowledge from the UMLS knowledge bases. Specifically, we extract entities from PubMed abstracts and link them to UMLS. We then train a knowledge-aware language model that firstly applies a text-only encoding layer to learn entity representation and applies a text-entity fusion encoding to aggregate entity representation. Besides, we add two training objectives as entity detection and entity linking. Experiments on the named entity recognition and relation extraction from the BLURB benchmark demonstrate the effectiveness of our approach. Further analysis on a collected probing dataset shows that our model has better ability to model medical knowledge.
Many facts come with an expiration date, from the name of the President to the basketball team Lebron James plays for. But language models (LMs) are trained on snapshots of data collected at a specific moment in time, and this can limit their utility, especially in the closed-book setting where the pretraining corpus must contain the facts the model should memorize. We introduce a diagnostic dataset aimed at probing LMs for factual knowledge that changes over time and highlight problems with LMs at either end of the spectrum -- those trained on specific slices of temporal data, as well as those trained on a wide range of temporal data. To mitigate these problems, we propose a simple technique for jointly modeling text with its timestamp. This improves memorization of seen facts from the training time period, as well as calibration on predictions about unseen facts from future time periods. We also show that models trained with temporal context can be efficiently ``refreshed as new data arrives, without the need for retraining from scratch.
Previous literatures show that pre-trained masked language models (MLMs) such as BERT can achieve competitive factual knowledge extraction performance on some datasets, indicating that MLMs can potentially be a reliable knowledge source. In this paper, we conduct a rigorous study to explore the underlying predicting mechanisms of MLMs over different extraction paradigms. By investigating the behaviors of MLMs, we find that previous decent performance mainly owes to the biased prompts which overfit dataset artifacts. Furthermore, incorporating illustrative cases and external contexts improve knowledge prediction mainly due to entity type guidance and golden answer leakage. Our findings shed light on the underlying predicting mechanisms of MLMs, and strongly question the previous conclusion that current MLMs can potentially serve as reliable factual knowledge bases.
Biomedical knowledge graphs (KGs) hold rich information on entities such as diseases, drugs, and genes. Predicting missing links in these graphs can boost many important applications, such as drug design and repurposing. Recent work has shown that general-domain language models (LMs) can serve as soft KGs, and that they can be fine-tuned for the task of KG completion. In this work, we study scientific LMs for KG completion, exploring whether we can tap into their latent knowledge to enhance biomedical link prediction. We evaluate several domain-specific LMs, fine-tuning them on datasets centered on drugs and diseases that we represent as KGs and enrich with textual entity descriptions. We integrate the LM-based models with KG embedding models, using a router method that learns to assign each input example to either type of model and provides a substantial boost in performance. Finally, we demonstrate the advantage of LM models in the inductive setting with novel scientific entities. Our datasets and code are made publicly available.
We introduce CoWeSe (the Corpus Web Salud Espa~nol), the largest Spanish biomedical corpus to date, consisting of 4.5GB (about 750M tokens) of clean plain text. CoWeSe is the result of a massive crawler on 3000 Spanish domains executed in 2020. The corpus is openly available and already preprocessed. CoWeSe is an important resource for biomedical and health NLP in Spanish and has already been employed to train domain-specific language models and to produce word embbedings. We released the CoWeSe corpus under a Creative Commons Attribution 4.0 International license, both in Zenodo (url{https://zenodo.org/record/4561971#.YTI5SnVKiEA}).
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