Infusing factual knowledge into pre-trained models is fundamental for many knowledge-intensive tasks. In this paper, we proposed Mixture-of-Partitions (MoP), an infusion approach that can handle a very large knowledge graph (KG) by partitioning it into smaller sub-graphs and infusing their specific knowledge into various BERT models using lightweight adapters. To leverage the overall factual knowledge for a target task, these sub-graph adapters are further fine-tuned along with the underlying BERT through a mixture layer. We evaluate our MoP with three biomedical BERTs (SciBERT, BioBERT, PubmedBERT) on six downstream tasks (inc. NLI, QA, Classification), and the results show that our MoP consistently enhances the underlying BERTs in task performance, and achieves new SOTA performances on five evaluated datasets.
Healthcare predictive analytics aids medical decision-making, diagnosis prediction and drug review analysis. Therefore, prediction accuracy is an important criteria which also necessitates robust predictive language models. However, the models using deep learning have been proven vulnerable towards insignificantly perturbed input instances which are less likely to be misclassified by humans. Recent efforts of generating adversaries using rule-based synonyms and BERT-MLMs have been witnessed in general domain, but the ever increasing biomedical literature poses unique challenges. We propose BBA…
Knowledge of a disease includes information of various aspects of the disease, such as signs and symptoms, diagnosis and treatment. This disease knowledge is critical for many health-related and biomedical tasks, including consumer health question answering, medical language inference and disease name recognition. While pre-trained language models like BERT have shown success in capturing syntactic, semantic, and world knowledge from text, we find they can be further complemented by specific information like knowledge of symptoms, diagnoses, treatments, and other disease aspects. Hence, we int…
Information Sciences Institute, University of Southern California（南加州大学信息科学研究所）；University of Southern California（南加州大学）
Stance detection infers a text author's attitude towards a target. This is challenging when the model lacks background knowledge about the target. Here, we show how background knowledge from Wikipedia can help enhance the performance on stance detection. We introduce Wikipedia Stance Detection BERT (WS-BERT) that infuses the knowledge into stance encoding. Extensive results on three benchmark datasets covering social media discussions and online debates indicate that our model significantly outperforms the state-of-the-art methods on target-specific stance detection, cross-target stance detect…
Contextualized entity representations learned by state-of-the-art transformer-based language models (TLMs) like BERT, GPT, T5, etc., leverage the attention mechanism to learn the data context from training data corpus. However, these models do not use the knowledge context. Knowledge context can be understood as semantics about entities and their relationship with neighboring entities in knowledge graphs. We propose a novel and effective technique to infuse knowledge context from multiple knowledge graphs for conceptual and ambiguous entities into TLMs during fine-tuning. It projects knowledge…
Department of Computer and Information Science University of Delaware（特拉华大学计算机与信息科学系）；University of Delaware（特拉华大学）；Department of Computer and Information Science（计算机与信息科学系）
With the explosive growth of biomedical literature, designing automatic tools to extract information from the literature has great significance in biomedical research. Recently, transformer-based BERT models adapted to the biomedical domain have produced leading results. However, all the existing BERT models for relation classification only utilize partial knowledge from the last layer. In this paper, we will investigate the method of utilizing the entire layer in the fine-tuning process of BERT model. To the best of our knowledge, we are the first to explore this method. The experimental resu…
The Ohio State University（俄亥俄州立大学）；National Library of Medicine（美国国家医学图书馆）；AI Institute, University of South Carolina（南卡罗来纳大学人工智能研究所）；George Washington University（乔治华盛顿大学）
The current UMLS (Unified Medical Language System) Metathesaurus construction process for integrating over 200 biomedical source vocabularies is expensive and error-prone as it relies on the lexical algorithms and human editors for deciding if the two biomedical terms are synonymous. Recent advances in Natural Language Processing such as Transformer models like BERT and its biomedical variants with contextualized word embeddings have achieved state-of-the-art (SOTA) performance on downstream tasks. We aim to validate if these approaches using the BERT models can actually outperform the existin…
National Center for Biotechnology Information（国家生物技术信息中心）；National Library of Medicine, National Institutes of Health（美国国立卫生研究院国家医学图书馆）
Inspired by the success of the General Language Understanding Evaluation benchmark, we introduce the Biomedical Language Understanding Evaluation (BLUE) benchmark to facilitate research in the development of pre-training language representations in the biomedicine domain. The benchmark consists of five tasks with ten datasets that cover both biomedical and clinical texts with different dataset sizes and difficulties. We also evaluate several baselines based on BERT and ELMo and find that the BERT model pre-trained on PubMed abstracts and MIMIC-III clinical notes achieves the best results. We m…
National Center for Biotechnology Information（国家生物技术信息中心）；National Library of Medicine, National Institutes of Health（美国国立卫生研究院国家医学图书馆）
Multi-task learning (MTL) has achieved remarkable success in natural language processing applications. In this work, we study a multi-task learning model with multiple decoders on varieties of biomedical and clinical natural language processing tasks such as text similarity, relation extraction, named entity recognition, and text inference. Our empirical results demonstrate that the MTL fine-tuned models outperform state-of-the-art transformer models (e.g., BERT and its variants) by 2.0% and 1.3% in biomedical and clinical domains, respectively. Pairwise MTL further demonstrates more details a…
Korea University（高丽大学）；Clova AI Research, Naver Corp（Naver公司Clova人工智能研究院）
Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recent…
University of Delaware（特拉华大学）；Weill Cornell Medicine（威尔康奈尔医学院）
Contrastive learning has been used to learn a high-quality representation of the image in computer vision. However, contrastive learning is not widely utilized in natural language processing due to the lack of a general method of data augmentation for text data. In this work, we explore the method of employing contrastive learning to improve the text representation from the BERT model for relation extraction. The key knob of our framework is a unique contrastive pre-training step tailored for the relation extraction tasks by seamlessly integrating linguistic knowledge into the data augmentatio…
Sun Yat-sen University（中山大学）；National Institutes of Health（美国国立卫生研究院）；University of Pennsylvania（宾夕法尼亚大学）
Pretrained language models such as Bidirectional Encoder Representations from Transformers (BERT) have achieved state-of-the-art performance in natural language processing (NLP) tasks. Recently, BERT has been adapted to the biomedical domain. Despite the effectiveness, these models have hundreds of millions of parameters and are computationally expensive when applied to large-scale NLP applications. We hypothesized that the number of parameters of the original BERT can be dramatically reduced with minor impact on performance. In this study, we present Bioformer, a compact BERT model for biomed…
In recent years, summarizers that incorporate domain knowledge into the process of text summarization have outperformed generic methods, especially for summarization of biomedical texts. However, construction and maintenance of domain knowledge bases are resource-intense tasks requiring significant manual annotation. In this paper, we demonstrate that contextualized representations extracted from the pre-trained deep language model BERT, can be effectively used to measure the similarity between sentences and to quantify the informative content. The results show that our BERT-based summarizer c…
Objective: This work aimed to demonstrate the effectiveness of a hybrid approach based on Sentence BERT model and retrofitting algorithm to compute relatedness between any two biomedical concepts. Materials and Methods: We generated concept vectors by encoding concept preferred terms using ELMo, BERT, and Sentence BERT models. We used BioELMo and Clinical ELMo. We used Ontology Knowledge Free (OKF) models like PubMedBERT, BioBERT, BioClinicalBERT, and Ontology Knowledge Injected (OKI) models like SapBERT, CoderBERT, KbBERT, and UmlsBERT. We trained all the BERT models using Siamese network on …
Dalian University of Technology（大连理工大学）；Beijing Institute of Health Administration and Medical Information（北京卫生健康经济研究和医学信息研究所）
Recognition of biomedical entities from literature is a challenging research focus, which is the foundation for extracting a large amount of biomedical knowledge existing in unstructured texts into structured formats. Using the sequence labeling framework to implement biomedical named entity recognition (BioNER) is currently a conventional method. This method, however, often cannot take full advantage of the semantic information in the dataset, and the performance is not always satisfactory. In this work, instead of treating the BioNER task as a sequence labeling problem, we formulate it as a …
Rutgers University–New Brunswick（罗格斯大学新伯朗士威校区）；Hasso Plattner Institute（哈索·普拉特纳研究所）；University of Potsdam（波茨坦大学）
Biomedical entity linking is the task of identifying mentions of biomedical concepts in text documents and mapping them to canonical entities in a target thesaurus. Recent advancements in entity linking using BERT-based models follow a retrieve and rerank paradigm, where the candidate entities are first selected using a retriever model, and then the retrieved candidates are ranked by a reranker model. While this paradigm produces state-of-the-art results, they are slow both at training and test time as they can process only one mention at a time. To mitigate these issues, we propose a BERT-bas…
National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH)（美国国家生物技术信息中心（NCBI）、美国国家医学图书馆（NLM）、美国国立卫生研究院（NIH））
A biomedical relation statement is commonly expressed in multiple sentences and consists of many concepts, including gene, disease, chemical, and mutation. To automatically extract information from biomedical literature, existing biomedical text-mining approaches typically formulate the problem as a cross-sentence n-ary relation-extraction task that detects relations among n entities across multiple sentences, and use either a graph neural network (GNN) with long short-term memory (LSTM) or an attention mechanism. Recently, Transformer has been shown to outperform LSTM on many natural language…
Manipal Institute of Technology（马尼帕尔理工学院）；Elsevier Labs（爱思唯尔实验室）
Biomedical Named Entity Recognition (NER) is a challenging problem in biomedical information processing due to the widespread ambiguity of out of context terms and extensive lexical variations. Performance on bioNER benchmarks continues to improve due to advances like BERT, GPT, and XLNet. FLAIR (1) is an alternative embedding model which is less computationally intensive than the others mentioned. We test FLAIR and its pretrained PubMed embeddings (which we term BioFLAIR) on a variety of bio NER tasks and compare those with results from BERT-type networks. We also investigate the effects of a…
School of Biomedical Informatics, The University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心生物医学信息学院）
Developing high-performance entity normalization algorithms that can alleviate the term variation problem is of great interest to the biomedical community. Although deep learning-based methods have been successfully applied to biomedical entity normalization, they often depend on traditional context-independent word embeddings. Bidirectional Encoder Representations from Transformers (BERT), BERT for Biomedical Text Mining (BioBERT) and BERT for Clinical Text Mining (ClinicalBERT) were recently introduced to pre-train contextualized word representation models using bidirectional Transformers, a…
University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Biomedical entity linking is the task of linking entity mentions in a biomedical document to referent entities in a knowledge base. Recently, many BERT-based models have been introduced for the task. While these models have achieved competitive results on many datasets, they are computationally expensive and contain about 110M parameters. Little is known about the factors contributing to their impressive performance and whether the over-parameterization is needed. In this work, we shed some light on the inner working mechanisms of these large BERT-based models. Through a set of probing experim…
Macquarie University（麦考瑞大学）；Australian National University（澳大利亚国立大学）
This paper presents the participation of Macquarie University and the Australian National University for Task B Phase B of the 2020 BioASQ Challenge (BioASQ8b). Our overall framework implements Query focused multi-document extractive summarisation by applying either a classification or a regression layer to the candidate sentence embeddings and to the comparison between the question and sentence embeddings. We experiment with variants using BERT and BioBERT, Siamese architectures, and reinforcement learning. We observe the best results when BERT is used to obtain the word embeddings, followed …
Loria, CNRS, Inria, Université de Lorraine（洛里亚研究所、法国国家科学研究中心、法国国家信息与自动化研究所、洛林大学）
Relation extraction (RE) consists in identifying and structuring automatically relations of interest from texts. Recently, BERT improved the top performances for several NLP tasks, including RE. However, the best way to use BERT, within a machine learning architecture, and within a transfer learning strategy is still an open question since it is highly dependent on each specific task and domain. Here, we explore various BERT-based architectures and transfer learning strategies (i.e., frozen or fine-tuned) for the task of biomedical RE on two corpora. Among tested architectures and strategies, …
BERT WEAVER: Using WEight AVERaging to enable lifelong learning for transformer-based models in biomedical semantic search engines
ZB MED - Information Centre for Life Sciences（ZB MED 生命科学信息中心）；Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI)（DILS 研究生院，比勒费尔德生物信息学基础设施研究所）；Faculty of Technology, Bielefeld University（比勒费尔德大学技术学院）；CITEC, Bielefeld University（比勒费尔德大学CITEC）；University of Bonn（波恩大学）
School of Biomedical Informatics, UT Health（UT Health生物医学信息学学院）
The rapid growth of biomedical literature poses a significant challenge for curation and interpretation. This has become more evident during the COVID-19 pandemic. LitCovid, a literature database of COVID-19 related papers in PubMed, has accumulated over 180,000 articles with millions of accesses. Approximately 10,000 new articles are added to LitCovid every month. A main curation task in LitCovid is topic annotation where an article is assigned with up to eight topics, e.g., Treatment and Diagnosis. The annotated topics have been widely used both in LitCovid (e.g., accounting for ~18% of tota…
We study the problem of injecting knowledge into large pre-trained models like BERT and RoBERTa. Existing methods typically update the original parameters of pre-trained models when injecting knowledge. However, when multiple kinds of knowledge are injected, the historically injected knowledge would be flushed away. To address this, we propose K-Adapter, a framework that retains the original parameters of the pre-trained model fixed and supports the development of versatile knowledge-infused model. Taking RoBERTa as the backbone model, K-Adapter has a neural adapter for each kind of infused kn…
PVminer: A Domain-Specific Tool to Detect the Patient Voice in Patient Generated Data
Department Of Emergency Medicine , Yale School of Medicine , 464 Congress Ave , 06519 , CT , USA；Department of Biomedical Informatics \& Data Science , Yale School of Medicine , 100 College Street , 06510 , CT , USA；Department of Social；Behavioral Sciences , Yale School of Public Health , 60 College Street , 06520 , CT , USA；Division of Research , Texas State University , 601 University Dr. , 78666 , TX , USA
Biomedical text mining is becoming increasingly important as the number of biomedical documents and web data rapidly grows. Recently, word representation models such as BERT has gained popularity among researchers. However, it is difficult to estimate their performance on datasets containing biomedical texts as the word distributions of general and biomedical corpora are quite different. Moreover, the medical domain has long-tail concepts and terminologies that are difficult to be learned via language models. For the Chinese biomedical text, it is more difficult due to its complex structure an…
Biomedical word embeddings are usually pre-trained on free text corpora with neural methods that capture local and global distributional properties. They are leveraged in downstream tasks using various neural architectures that are designed to optimize task-specific objectives that might further tune such embeddings. Since 2018, however, there is a marked shift from these static embeddings to contextual embeddings motivated by language models (e.g., ELMo, transformers such as BERT, and ULMFiT). These dynamic embeddings have the added benefit of being able to distinguish homonyms and acronyms g…
In this research, we present our work participation for the DrugProt task of BioCreative VII challenge. Drug-target interactions (DTIs) are critical for drug discovery and repurposing, which are often manually extracted from the experimental articles. There are >32M biomedical articles on PubMed and manually extracting DTIs from such a huge knowledge base is challenging. To solve this issue, we provide a solution for Track 1, which aims to extract 10 types of interactions between drug and protein entities. We applied an Ensemble Classifier model that combines BioMed-RoBERTa, a state of art lan…
Motivation: A perennial challenge for biomedical researchers and clinical practitioners is to stay abreast with the rapid growth of publications and medical notes. Natural language processing (NLP) has emerged as a promising direction for taming information overload. In particular, large neural language models facilitate transfer learning by pretraining on unlabeled text, as exemplified by the successes of BERT models in various NLP applications. However, fine-tuning such models for an end task remains challenging, especially with small labeled datasets, which are common in biomedical NLP. Res…
This paper presents several BERT-based models for Russian language biomedical text mining (RuBioBERT, RuBioRoBERTa). The models are pre-trained on a corpus of freely available texts in the Russian biomedical domain. With this pre-training, our models demonstrate state-of-the-art results on RuMedBench - Russian medical language understanding benchmark that covers a diverse set of tasks, including text classification, question answering, natural language inference, and named entity recognition.
Off-the-shelf biomedical embeddings obtained from the recently released various pre-trained language models (such as BERT, XLNET) have demonstrated state-of-the-art results (in terms of accuracy) for the various natural language understanding tasks (NLU) in the biomedical domain. Relation Classification (RC) falls into one of the most critical tasks. In this paper, we explore how to incorporate domain knowledge of the biomedical entities (such as drug, disease, genes), obtained from Knowledge Graph (KG) Embeddings, for predicting Drug-Drug Interaction from textual corpus. We propose a new meth…
Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing assumption is that even domain-specific pretraining can benefit by starting from general-domain language models. In this paper, we challenge this assumption by showing that for domains with abundant unlabeled text, such as biomedicine, pretraining language models from scratch results in substantial gains over continual pretraining of general-domain language m…
Dalian University of Technology（大连理工大学）；Beijing Institute of Health Administration and Medical Information（北京卫生健康管理与医学信息研究所）
Motivation: The biomedical literature contains a wealth of chemical-protein interactions (CPIs). Automatically extracting CPIs described in biomedical literature is essential for drug discovery, precision medicine, as well as basic biomedical research. Most existing methods focus only on the sentence sequence to identify these CPIs. However, the local structure of sentences and external biomedical knowledge also contain valuable information. Effective use of such information may improve the performance of CPI extraction. Results: In this paper, we propose a novel neural network-based approach …
German Research Center for Artificial Intelligence (DFKI)（德国人工智能研究中心）
Fact triples are a common form of structured knowledge used within the biomedical domain. As the amount of unstructured scientific texts continues to grow, manual annotation of these texts for the task of relation extraction becomes increasingly expensive. Distant supervision offers a viable approach to combat this by quickly producing large amounts of labeled, but considerably noisy, data. We aim to reduce such noise by extending an entity-enriched relation classification BERT model to the problem of multiple instance learning, and defining a simple data encoding scheme that significantly red…
AI-assisted Knowledge Discovery in Biomedical Literature to Support Decision-making in Precision Oncology
Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine（约翰斯·霍普金斯大学医学院西德尼·金梅尔综合癌症中心）；Johns Hopkins School of Medicine（约翰斯·霍普金斯大学医学院）
Scalable Construction of a Lung Cancer Knowledge Base: Profiling Semantic Reasoning in LLMs
Universidad Tecnológica de la Mixteca（拉巴斯技术大学）；Instituto Nacional de Enfermedades Respiratorias (INER) Ismael Cosío Villegas（国家呼吸疾病研究所（INER）伊斯梅尔·科索·维利亚斯）；Maynooth University（梅诺特大学）
University of Minnesota（明尼苏达大学）；University of Illinois（伊利诺伊大学）；The University of Manchester（曼彻斯特大学）；Pontifical Catholic University of Rio de Janeiro（里约热内卢天主教大学）；The University of Texas Health Science Center at Houston（德克萨斯大学休斯顿健康科学中心）
OBJECTIVE: Leverage existing biomedical NLP tools and DS domain terminology to produce a novel and comprehensive knowledge graph containing dietary supplement (DS) information for discovering interactions between DS and drugs, or Drug-Supplement Interactions (DSI). MATERIALS AND METHODS: We created SemRepDS (an extension of SemRep), capable of extracting semantic relations from abstracts by leveraging a DS-specific terminology (iDISK) containing 28,884 DS terms not found in the UMLS. PubMed abstracts were processed using SemRepDS to generate semantic relations, which were then filtered using a…
BioPars: A Pretrained Biomedical Large Language Model for Persian Biomedical Text Mining
Department of Computer Science, Faculty of Education, University of Kufa（计算机科学系，教育学院，科菲大学）；Department of Computer Science, Florida State University（计算机科学系，佛罗里达州立大学）；Department of Computer Engineering, Velayat University（计算机工程系，瓦莱yat大学）；Department of Mechanical Engineering, Amirkabir University of Technology（机械工程系，阿米卡比尔技术大学）；Department of Computer Engineering, Ferdowsi University of Mashhad（计算机工程系，法尔德大学）
University of Texas Health Science Center at Houston（休斯顿德克萨斯大学健康科学中心）；University of Minnesota（明尼苏达大学）；University of Pennsylvania（宾夕法尼亚大学）；University of Maryland School of Medicine（马里兰大学医学院）
To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leveraged in many biomedical applications including drug repurposing. Our objective is to construct a knowledge graph from literature to study relations between Alzheimer's disease (AD) and chemicals, drugs and dietary supplements in order to identify opportunities to prevent or delay neurodegenerative progression. We collected biomedical annotations and extracted their relations using SemRep vi…
