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Register a new userScientific Language Models for Biomedical Knowledge Base Completion: An Empirical Study
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Added by
Rahul Nadkarni
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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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.
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Scaling existing applications and solutions to multiple human languages has traditionally proven to be difficult, mainly due to the language-dependent nature of preprocessing and feature engineering techniques employed in traditional approaches. In this work, we empirically investigate the factors affecting language-independent models built with multilingual representations, including task type, language set and data resource. On two most representative NLP tasks -- sentence classification and sequence labeling, we show that language-independent models can be comparable to or even outperforms the models trained using monolingual data, and they are generally more effective on sentence classification. We experiment language-independent models with many different languages and show that they are more suitable for typologically similar languages. We also explore the effects of different data sizes when training and testing language-independent models, and demonstrate that they are not only suitable for high-resource languages, but also very effective in low-resource languages.
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.
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.
In logic-based approaches to reasoning tasks such as Recognizing Textual Entailment (RTE), it is important for a system to have a large amount of knowledge data. However, there is a tradeoff between adding more knowledge data for improved RTE performance and maintaining an efficient RTE system, as such a big database is problematic in terms of the memory usage and computational complexity. In this work, we show the processing time of a state-of-the-art logic-based RTE system can be significantly reduced by replacing its search-based axiom injection (abduction) mechanism by that based on Knowledge Base Completion (KBC). We integrate this mechanism in a Coq plugin that provides a proof automation tactic for natural language inference. Additionally, we show empirically that adding new knowledge data contributes to better RTE performance while not harming the processing speed in this framework.
Automatic construction of relevant Knowledge Bases (KBs) from text, and generation of semantically meaningful text from KBs are both long-standing goals in Machine Learning. In this paper, we present ReGen, a bidirectional generation of text and graph leveraging Reinforcement Learning (RL) to improve performance. Graph linearization enables us to re-frame both tasks as a sequence to sequence generation problem regardless of the generative direction, which in turn allows the use of Reinforcement Learning for sequence training where the model itself is employed as its own critic leading to Self-Critical Sequence Training (SCST). We present an extensive investigation demonstrating that the use of RL via SCST benefits graph and text generation on WebNLG+ 2020 and TekGen datasets. Our system provides state-of-the-art results on WebNLG+ 2020 by significantly improving upon published results from the WebNLG 2020+ Challenge for both text-to-graph and graph-to-text generation tasks.
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