Hua Xu

Hanlei Zhang, Hua Xu, Xin Wang et al. · tsinghua

Multimodal intent recognition is a significant task for understanding human language in real-world multimodal scenes. Most existing intent recognition methods have limitations in leveraging the multimodal information due to the restrictions of the benchmark datasets with only text information. This paper introduces a novel dataset for multimodal intent recognition (MIntRec) to address this issue. It formulates coarse-grained and fine-grained intent taxonomies based on the data collected from the TV series Superstore. The dataset consists of 2,224 high-quality samples with text, video, and audio modalities and has multimodal annotations among twenty intent categories. Furthermore, we provide annotated bounding boxes of speakers in each video segment and achieve an automatic process for speaker annotation. MIntRec is helpful for researchers to mine relationships between different modalities to enhance the capability of intent recognition. We extract features from each modality and model cross-modal interactions by adapting three powerful multimodal fusion methods to build baselines. Extensive experiments show that employing the non-verbal modalities achieves substantial improvements compared with the text-only modality, demonstrating the effectiveness of using multimodal information for intent recognition. The gap between the best-performing methods and humans indicates the challenge and importance of this task for the community. The full dataset and codes are available for use at https://github.com/thuiar/MIntRec.

Rui Yang, Qingcheng Zeng, Keen You et al.

This study introduces Ascle, a pioneering natural language processing (NLP) toolkit designed for medical text generation. Ascle is tailored for biomedical researchers and healthcare professionals with an easy-to-use, all-in-one solution that requires minimal programming expertise. For the first time, Ascle evaluates and provides interfaces for the latest pre-trained language models, encompassing four advanced and challenging generative functions: question-answering, text summarization, text simplification, and machine translation. In addition, Ascle integrates 12 essential NLP functions, along with query and search capabilities for clinical databases. The toolkit, its models, and associated data are publicly available via https://github.com/Yale-LILY/MedGen.

Cathy Shyr, Yan Hu, Paul A. Harris et al.

Rare diseases (RDs) are collectively common and affect 300 million people worldwide. Accurate phenotyping is critical for informing diagnosis and treatment, but RD phenotypes are often embedded in unstructured text and time-consuming to extract manually. While natural language processing (NLP) models can perform named entity recognition (NER) to automate extraction, a major bottleneck is the development of a large, annotated corpus for model training. Recently, prompt learning emerged as an NLP paradigm that can lead to more generalizable results without any (zero-shot) or few labeled samples (few-shot). Despite growing interest in ChatGPT, a revolutionary large language model capable of following complex human prompts and generating high-quality responses, none have studied its NER performance for RDs in the zero- and few-shot settings. To this end, we engineered novel prompts aimed at extracting RD phenotypes and, to the best of our knowledge, are the first the establish a benchmark for evaluating ChatGPT's performance in these settings. We compared its performance to the traditional fine-tuning approach and conducted an in-depth error analysis. Overall, fine-tuning BioClinicalBERT resulted in higher performance (F1 of 0.689) than ChatGPT (F1 of 0.472 and 0.591 in the zero- and few-shot settings, respectively). Despite this, ChatGPT achieved similar or higher accuracy for certain entities (i.e., rare diseases and signs) in the one-shot setting (F1 of 0.776 and 0.725). This suggests that with appropriate prompt engineering, ChatGPT has the potential to match or outperform fine-tuned language models for certain entity types with just one labeled sample. While the proliferation of large language models may provide opportunities for supporting RD diagnosis and treatment, researchers and clinicians should critically evaluate model outputs and be well-informed of their limitations.

Hanlei Zhang, Hua Xu, Shaojie Zhao et al. · tsinghua

Open intent detection is a significant problem in natural language understanding, which aims to identify the unseen open intent while ensuring known intent identification performance. However, current methods face two major challenges. Firstly, they struggle to learn friendly representations to detect the open intent with prior knowledge of only known intents. Secondly, there is a lack of an effective approach to obtaining specific and compact decision boundaries for known intents. To address these issues, this paper presents an original framework called DA-ADB, which successively learns distance-aware intent representations and adaptive decision boundaries for open intent detection. Specifically, we first leverage distance information to enhance the distinguishing capability of the intent representations. Then, we design a novel loss function to obtain appropriate decision boundaries by balancing both empirical and open space risks. Extensive experiments demonstrate the effectiveness of the proposed distance-aware and boundary learning strategies. Compared to state-of-the-art methods, our framework achieves substantial improvements on three benchmark datasets. Furthermore, it yields robust performance with varying proportions of labeled data and known categories.

Yihe Liu, Ziqi Yuan, Huisheng Mao et al.

Multimodal sentiment analysis (MSA), which supposes to improve text-based sentiment analysis with associated acoustic and visual modalities, is an emerging research area due to its potential applications in Human-Computer Interaction (HCI). However, the existing researches observe that the acoustic and visual modalities contribute much less than the textual modality, termed as text-predominant. Under such circumstances, in this work, we emphasize making non-verbal cues matter for the MSA task. Firstly, from the resource perspective, we present the CH-SIMS v2.0 dataset, an extension and enhancement of the CH-SIMS. Compared with the original dataset, the CH-SIMS v2.0 doubles its size with another 2121 refined video segments with both unimodal and multimodal annotations and collects 10161 unlabelled raw video segments with rich acoustic and visual emotion-bearing context to highlight non-verbal cues for sentiment prediction. Secondly, from the model perspective, benefiting from the unimodal annotations and the unsupervised data in the CH-SIMS v2.0, the Acoustic Visual Mixup Consistent (AV-MC) framework is proposed. The designed modality mixup module can be regarded as an augmentation, which mixes the acoustic and visual modalities from different videos. Through drawing unobserved multimodal context along with the text, the model can learn to be aware of different non-verbal contexts for sentiment prediction. Our evaluations demonstrate that both CH-SIMS v2.0 and AV-MC framework enables further research for discovering emotion-bearing acoustic and visual cues and paves the path to interpretable end-to-end HCI applications for real-world scenarios.

Kang Zhao, Hua Xu, Jiangong Yang et al.

Continual relation extraction (CRE) aims to continuously train a model on data with new relations while avoiding forgetting old ones. Some previous work has proved that storing a few typical samples of old relations and replaying them when learning new relations can effectively avoid forgetting. However, these memory-based methods tend to overfit the memory samples and perform poorly on imbalanced datasets. To solve these challenges, a consistent representation learning method is proposed, which maintains the stability of the relation embedding by adopting contrastive learning and knowledge distillation when replaying memory. Specifically, supervised contrastive learning based on a memory bank is first used to train each new task so that the model can effectively learn the relation representation. Then, contrastive replay is conducted of the samples in memory and makes the model retain the knowledge of historical relations through memory knowledge distillation to prevent the catastrophic forgetting of the old task. The proposed method can better learn consistent representations to alleviate forgetting effectively. Extensive experiments on FewRel and TACRED datasets show that our method significantly outperforms state-of-the-art baselines and yield strong robustness on the imbalanced dataset.

Zehan Li, Yan Hu, Scott Lane et al.

Accurate identification and categorization of suicidal events can yield better suicide precautions, reducing operational burden, and improving care quality in high-acuity psychiatric settings. Pre-trained language models offer promise for identifying suicidality from unstructured clinical narratives. We evaluated the performance of four BERT-based models using two fine-tuning strategies (multiple single-label and single multi-label) for detecting coexisting suicidal events from 500 annotated psychiatric evaluation notes. The notes were labeled for suicidal ideation (SI), suicide attempts (SA), exposure to suicide (ES), and non-suicidal self-injury (NSSI). RoBERTa outperformed other models using multiple single-label classification strategy (acc=0.86, F1=0.78). MentalBERT (acc=0.83, F1=0.74) also exceeded BioClinicalBERT (acc=0.82, F1=0.72) which outperformed BERT (acc=0.80, F1=0.70). RoBERTa fine-tuned with single multi-label classification further improved the model performance (acc=0.88, F1=0.81). The findings highlight that the model optimization, pretraining with domain-relevant data, and the single multi-label classification strategy enhance the model performance of suicide phenotyping. Keywords: EHR-based Phenotyping; Natural Language Processing; Secondary Use of EHR Data; Suicide Classification; BERT-based Model; Psychiatry; Mental Health

Kaicheng Yang, Ruxuan Zhang, Hua Xu et al.

Inter-modal interaction plays an indispensable role in multimodal sentiment analysis. Due to different modalities sequences are usually non-alignment, how to integrate relevant information of each modality to learn fusion representations has been one of the central challenges in multimodal learning. In this paper, a Self-Adjusting Fusion Representation Learning Model (SA-FRLM) is proposed to learn robust crossmodal fusion representations directly from the unaligned text and audio sequences. Different from previous works, our model not only makes full use of the interaction between different modalities but also maximizes the protection of the unimodal characteristics. Specifically, we first employ a crossmodal alignment module to project different modalities features to the same dimension. The crossmodal collaboration attention is then adopted to model the inter-modal interaction between text and audio sequences and initialize the fusion representations. After that, as the core unit of the SA-FRLM, the crossmodal adjustment transformer is proposed to protect original unimodal characteristics. It can dynamically adapt the fusion representations by using single modal streams. We evaluate our approach on the public multimodal sentiment analysis datasets CMU-MOSI and CMU-MOSEI. The experiment results show that our model has significantly improved the performance of all the metrics on the unaligned text-audio sequences.

Yan Hu, Qingyu Chen, Jingcheng Du et al.

Objective: This study quantifies the capabilities of GPT-3.5 and GPT-4 for clinical named entity recognition (NER) tasks and proposes task-specific prompts to improve their performance. Materials and Methods: We evaluated these models on two clinical NER tasks: (1) to extract medical problems, treatments, and tests from clinical notes in the MTSamples corpus, following the 2010 i2b2 concept extraction shared task, and (2) identifying nervous system disorder-related adverse events from safety reports in the vaccine adverse event reporting system (VAERS). To improve the GPT models' performance, we developed a clinical task-specific prompt framework that includes (1) baseline prompts with task description and format specification, (2) annotation guideline-based prompts, (3) error analysis-based instructions, and (4) annotated samples for few-shot learning. We assessed each prompt's effectiveness and compared the models to BioClinicalBERT. Results: Using baseline prompts, GPT-3.5 and GPT-4 achieved relaxed F1 scores of 0.634, 0.804 for MTSamples, and 0.301, 0.593 for VAERS. Additional prompt components consistently improved model performance. When all four components were used, GPT-3.5 and GPT-4 achieved relaxed F1 socres of 0.794, 0.861 for MTSamples and 0.676, 0.736 for VAERS, demonstrating the effectiveness of our prompt framework. Although these results trail BioClinicalBERT (F1 of 0.901 for the MTSamples dataset and 0.802 for the VAERS), it is very promising considering few training samples are needed. Conclusion: While direct application of GPT models to clinical NER tasks falls short of optimal performance, our task-specific prompt framework, incorporating medical knowledge and training samples, significantly enhances GPT models' feasibility for potential clinical applications.

Huigen Ye, Hongyan Wang, Hua Xu et al.

Integer programming problems (IPs) are challenging to be solved efficiently due to the NP-hardness, especially for large-scale IPs. To solve this type of IPs, Large neighborhood search (LNS) uses an initial feasible solution and iteratively improves it by searching a large neighborhood around the current solution. However, LNS easily steps into local optima and ignores the correlation between variables to be optimized, leading to compromised performance. This paper presents a general adaptive constraint partition-based optimization framework (ACP) for large-scale IPs that can efficiently use any existing optimization solver as a subroutine. Specifically, ACP first randomly partitions the constraints into blocks, where the number of blocks is adaptively adjusted to avoid local optima. Then, ACP uses a subroutine solver to optimize the decision variables in a randomly selected block of constraints to enhance the variable correlation. ACP is compared with LNS framework with different subroutine solvers on four IPs and a real-world IP. The experimental results demonstrate that in specified wall-clock time ACP shows better performance than SCIP and Gurobi.

Zhijing Wu, Hua Xu, Jingliang Fang et al.

Continual Machine Reading Comprehension aims to incrementally learn from a continuous data stream across time without access the previous seen data, which is crucial for the development of real-world MRC systems. However, it is a great challenge to learn a new domain incrementally without catastrophically forgetting previous knowledge. In this paper, MA-MRC, a continual MRC model with uncertainty-aware fixed Memory and Adversarial domain adaptation, is proposed. In MA-MRC, a fixed size memory stores a small number of samples in previous domain data along with an uncertainty-aware updating strategy when new domain data arrives. For incremental learning, MA-MRC not only keeps a stable understanding by learning both memory and new domain data, but also makes full use of the domain adaptation relationship between them by adversarial learning strategy. The experimental results show that MA-MRC is superior to strong baselines and has a substantial incremental learning ability without catastrophically forgetting under two different continual MRC settings.

Xiang Xue, Yatu Ji, Qing-dao-er-ji Ren et al.

Logit Knowledge Distillation has gained substantial research interest in recent years due to its simplicity and lack of requirement for intermediate feature alignment; however, it suffers from limited interpretability in its decision-making process. To address this, we propose implicit Clustering Distillation (iCD): a simple and effective method that mines and transfers interpretable structural knowledge from logits, without requiring ground-truth labels or feature-space alignment. iCD leverages Gram matrices over decoupled local logit representations to enable student models to learn latent semantic structural patterns. Extensive experiments on benchmark datasets demonstrate the effectiveness of iCD across diverse teacher-student architectures, with particularly strong performance in fine-grained classification tasks -- achieving a peak improvement of +5.08% over the baseline. The code is available at: https://github.com/maomaochongaa/iCD.

Zhangyi Hu, Jiemin Wu, Hua Xu et al.

Irregular Multivariate Time Series (IMTS) forecasting is challenging due to the unaligned nature of multi-channel signals and the prevalence of extensive missing data. Existing methods struggle to capture reliable temporal patterns from such data due to significant missing values. While pre-trained foundation models show potential for addressing these challenges, they are typically designed for Regularly Sampled Time Series (RTS). Motivated by the visual Mask AutoEncoder's (MAE) powerful capability for modeling sparse multi-channel information and its success in RTS forecasting, we propose VIMTS, a framework adapting Visual MAE for IMTS forecasting. To mitigate the effect of missing values, VIMTS first processes IMTS along the timeline into feature patches at equal intervals. These patches are then complemented using learned cross-channel dependencies. Then it leverages visual MAE's capability in handling sparse multichannel data for patch reconstruction, followed by a coarse-to-fine technique to generate precise predictions from focused contexts. In addition, we integrate self-supervised learning for improved IMTS modeling by adapting the visual MAE to IMTS data. Extensive experiments demonstrate VIMTS's superior performance and few-shot capability, advancing the application of visual foundation models in more general time series tasks. Our code is available at https://github.com/WHU-HZY/VIMTS.

Tianyu Liu, Yijia Xiao, Xiao Luo et al.

The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs to genomics and proteomics is still limited. To fill this gap, we propose a collection of finetuned LLMs and multimodal LLMs (MLLMs), known as Geneverse, for three novel tasks in genomic and proteomic research. The models in Geneverse are trained and evaluated based on domain-specific datasets, and we use advanced parameter-efficient finetuning techniques to achieve the model adaptation for tasks including the generation of descriptions for gene functions, protein function inference from its structure, and marker gene selection from spatial transcriptomic data. We demonstrate that adapted LLMs and MLLMs perform well for these tasks and may outperform closed-source large-scale models based on our evaluations focusing on both truthfulness and structural correctness. All of the training strategies and base models we used are freely accessible.

Qingyu Chen, Yan Hu, Xueqing Peng et al.

The rapid growth of biomedical literature poses challenges for manual knowledge curation and synthesis. Biomedical Natural Language Processing (BioNLP) automates the process. While Large Language Models (LLMs) have shown promise in general domains, their effectiveness in BioNLP tasks remains unclear due to limited benchmarks and practical guidelines. We perform a systematic evaluation of four LLMs, GPT and LLaMA representatives on 12 BioNLP benchmarks across six applications. We compare their zero-shot, few-shot, and fine-tuning performance with traditional fine-tuning of BERT or BART models. We examine inconsistencies, missing information, hallucinations, and perform cost analysis. Here we show that traditional fine-tuning outperforms zero or few shot LLMs in most tasks. However, closed-source LLMs like GPT-4 excel in reasoning-related tasks such as medical question answering. Open source LLMs still require fine-tuning to close performance gaps. We find issues like missing information and hallucinations in LLM outputs. These results offer practical insights for applying LLMs in BioNLP.

Mingchen Li, Halil Kilicoglu, Hua Xu et al.

Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues such as generating inaccurate information or hallucinations. Retrieval-augmented generation provided a solution for these models to update knowledge and enhance their performance. In contrast to previous retrieval-augmented LMs, which utilize specialized cross-attention mechanisms to help LLM encode retrieved text, BiomedRAG adopts a simpler approach by directly inputting the retrieved chunk-based documents into the LLM. This straightforward design is easily applicable to existing retrieval and language models, effectively bypassing noise information in retrieved documents, particularly in noise-intensive tasks. Moreover, we demonstrate the potential for utilizing the LLM to supervise the retrieval model in the biomedical domain, enabling it to retrieve the document that assists the LM in improving its predictions. Our experiments reveal that with the tuned scorer,\textsc{ BiomedRAG} attains superior performance across 5 biomedical NLP tasks, encompassing information extraction (triple extraction, relation extraction), text classification, link prediction, and question-answering, leveraging over 9 datasets. For instance, in the triple extraction task, \textsc{BiomedRAG} outperforms other triple extraction systems with micro-F1 scores of 81.42 and 88.83 on GIT and ChemProt corpora, respectively.

Yiming Li, Xueqing Peng, Jianfu Li et al.

In acupuncture therapy, the accurate location of acupoints is essential for its effectiveness. The advanced language understanding capabilities of large language models (LLMs) like Generative Pre-trained Transformers (GPT) present a significant opportunity for extracting relations related to acupoint locations from textual knowledge sources. This study aims to compare the performance of GPT with traditional deep learning models (Long Short-Term Memory (LSTM) and Bidirectional Encoder Representations from Transformers for Biomedical Text Mining (BioBERT)) in extracting acupoint-related location relations and assess the impact of pretraining and fine-tuning on GPT's performance. We utilized the World Health Organization Standard Acupuncture Point Locations in the Western Pacific Region (WHO Standard) as our corpus, which consists of descriptions of 361 acupoints. Five types of relations ('direction_of,' 'distance_of,' 'part_of,' 'near_acupoint,' and 'located_near') (n= 3,174) between acupoints were annotated. Five models were compared: BioBERT, LSTM, pre-trained GPT-3.5, fine-tuned GPT-3.5, as well as pre-trained GPT-4. Performance metrics included micro-average exact match precision, recall, and F1 scores. Our results demonstrate that fine-tuned GPT-3.5 consistently outperformed other models in F1 scores across all relation types. Overall, it achieved the highest micro-average F1 score of 0.92. This study underscores the effectiveness of LLMs like GPT in extracting relations related to acupoint locations, with implications for accurately modeling acupuncture knowledge and promoting standard implementation in acupuncture training and practice. The findings also contribute to advancing informatics applications in traditional and complementary medicine, showcasing the potential of LLMs in natural language processing.

Rongbin Li, Wenbo Chen, Jinbo Li et al.

By leveraging GPT-4 for ontology narration, we developed GPTON to infuse structured knowledge into LLMs through verbalized ontology terms, achieving accurate text and ontology annotations for over 68% of gene sets in the top five predictions. Manual evaluations confirm GPTON's robustness, highlighting its potential to harness LLMs and structured knowledge to significantly advance biomedical research beyond gene set annotation.

Gongbo Zhang, Yiliang Zhou, Yan Hu et al.

Objectives Extraction of PICO (Populations, Interventions, Comparison, and Outcomes) entities is fundamental to evidence retrieval. We present a novel method PICOX to extract overlapping PICO entities. Materials and Methods PICOX first identifies entities by assessing whether a word marks the beginning or conclusion of an entity. Then it uses a multi-label classifier to assign one or more PICO labels to a span candidate. PICOX was evaluated using one of the best-performing baselines, EBM-NLP, and three more datasets, i.e., PICO-Corpus, and RCT publications on Alzheimer's Disease or COVID-19, using entity-level precision, recall, and F1 scores. Results PICOX achieved superior precision, recall, and F1 scores across the board, with the micro F1 score improving from 45.05 to 50.87 (p << 0.01). On the PICO-Corpus, PICOX obtained higher recall and F1 scores than the baseline and improved the micro recall score from 56.66 to 67.33. On the COVID-19 dataset, PICOX also outperformed the baseline and improved the micro F1 score from 77.10 to 80.32. On the AD dataset, PICOX demonstrated comparable F1 scores with higher precision when compared to the baseline. Conclusion PICOX excels in identifying overlapping entities and consistently surpasses a leading baseline across multiple datasets. Ablation studies reveal that its data augmentation strategy effectively minimizes false positives and improves precision.

Huixue Zhou, Robin Austin, Sheng-Chieh Lu et al.

Objective: Our study aimed to construct an exhaustive Complementary and Integrative Health (CIH) Lexicon (CIHLex) to better represent the often underrepresented physical and psychological CIH approaches in standard terminologies. We also intended to apply advanced Natural Language Processing (NLP) models such as Bidirectional Encoder Representations from Transformers (BERT) and GPT-3.5 Turbo for CIH named entity recognition, evaluating their performance against established models like MetaMap and CLAMP. Materials and Methods: We constructed the CIHLex by integrating various resources, compiling and integrating data from biomedical literature and relevant knowledge bases. The Lexicon encompasses 198 unique concepts with 1090 corresponding unique terms. We matched these concepts to the Unified Medical Language System (UMLS). Additionally, we developed and utilized BERT models and compared their efficiency in CIH named entity recognition to that of other models such as MetaMap, CLAMP, and GPT3.5-turbo. Results: From the 198 unique concepts in CIHLex, 62.1% could be matched to at least one term in the UMLS. Moreover, 75.7% of the mapped UMLS Concept Unique Identifiers (CUIs) were categorized as "Therapeutic or Preventive Procedure." Among the models applied to CIH named entity recognition, BLUEBERT delivered the highest macro average F1-score of 0.90, surpassing other models. Conclusion: Our CIHLex significantly augments representation of CIH approaches in biomedical literature. Demonstrating the utility of advanced NLP models, BERT notably excelled in CIH entity recognition. These results highlight promising strategies for enhancing standardization and recognition of CIH terminology in biomedical contexts.

Greg M. Silverman, Raymond L. Finzel, Michael V. Heinz et al.

Our objective in this study is to investigate the behavior of Boolean operators on combining annotation output from multiple Natural Language Processing (NLP) systems across multiple corpora and to assess how filtering by aggregation of Unified Medical Language System (UMLS) Metathesaurus concepts affects system performance for Named Entity Recognition (NER) of UMLS concepts. We used three corpora annotated for UMLS concepts: 2010 i2b2 VA challenge set (31,161 annotations), Multi-source Integrated Platform for Answering Clinical Questions (MiPACQ) corpus (17,457 annotations including UMLS concept unique identifiers), and Fairview Health Services corpus (44,530 annotations). Our results showed that for UMLS concept matching, Boolean ensembling of the MiPACQ corpus trended towards higher performance over individual systems. Use of an approximate grid-search can help optimize the precision-recall tradeoff and can provide a set of heuristics for choosing an optimal set of ensembles.

Dalton Schutte, Jake Vasilakes, Anu Bompelli et al.

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 PubMedBERT-based model to remove incorrect relations before generating our knowledge graph (SuppKG). Two pathways are used to identify potential DS-Drug interactions which are then evaluated by medical professionals for mechanistic plausibility. RESULTS: Comparison analysis found that SemRepDS returned 206.9% more DS relations and 158.5% more DS entities than SemRep. The fine-tuned BERT model obtained an F1 score of 0.8605 and removed 43.86% of the relations, improving the precision of the relations by 26.4% compared to pre-filtering. SuppKG consists of 2,928 DS-specific nodes. Manual review of findings identified 44 (88%) proposed DS-Gene-Drug and 32 (64%) proposed DS-Gene1-Function-Gene2-Drug pathways to be mechanistically plausible. DISCUSSION: The additional relations extracted using SemRepDS generated SuppKG that was used to find plausible DSI not found in the current literature. By the nature of the SuppKG, these interactions are unlikely to have been found using SemRep without the expanded DS terminology. CONCLUSION: We successfully extend SemRep to include DS information and produce SuppKG which can be used to find potential DS-Drug interactions.

Jingqi Wang, Noor Abu-el-rub, Josh Gray et al.

The COVID-19 pandemic swept across the world rapidly, infecting millions of people. An efficient tool that can accurately recognize important clinical concepts of COVID-19 from free text in electronic health records (EHRs) will be valuable to accelerate COVID-19 clinical research. To this end, this study aims at adapting the existing CLAMP natural language processing tool to quickly build COVID-19 SignSym, which can extract COVID-19 signs/symptoms and their 8 attributes (body location, severity, temporal expression, subject, condition, uncertainty, negation, and course) from clinical text. The extracted information is also mapped to standard concepts in the Observational Medical Outcomes Partnership common data model. A hybrid approach of combining deep learning-based models, curated lexicons, and pattern-based rules was applied to quickly build the COVID-19 SignSym from CLAMP, with optimized performance. Our extensive evaluation using 3 external sites with clinical notes of COVID-19 patients, as well as the online medical dialogues of COVID-19, shows COVID-19 Sign-Sym can achieve high performance across data sources. The workflow used for this study can be generalized to other use cases, where existing clinical natural language processing tools need to be customized for specific information needs within a short time. COVID-19 SignSym is freely accessible to the research community as a downloadable package (https://clamp.uth.edu/covid/nlp.php) and has been used by 16 healthcare organizations to support clinical research of COVID-19.

Hong Guan, Jianfu Li, Hua Xu et al.

Background: Identifying relationships between clinical events and temporal expressions is a key challenge in meaningfully analyzing clinical text for use in advanced AI applications. While previous studies exist, the state-of-the-art performance has significant room for improvement. Methods: We studied several variants of BERT (Bidirectional Encoder Representations using Transformers) some involving clinical domain customization and the others involving improved architecture and/or training strategies. We evaluated these methods using a direct temporal relations dataset which is a semantically focused subset of the 2012 i2b2 temporal relations challenge dataset. Results: Our results show that RoBERTa, which employs better pre-training strategies including using 10x larger corpus, has improved overall F measure by 0.0864 absolute score (on the 1.00 scale) and thus reducing the error rate by 24% relative to the previous state-of-the-art performance achieved with an SVM (support vector machine) model. Conclusion: Modern contextual language modeling neural networks, pre-trained on a large corpus, achieve impressive performance even on highly-nuanced clinical temporal relation tasks.

Zongcheng Ji, Qiang Wei, Hua Xu

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, advancing the state-of-the-art for many natural language processing tasks. In this study, we proposed an entity normalization architecture by fine-tuning the pre-trained BERT / BioBERT / ClinicalBERT models and conducted extensive experiments to evaluate the effectiveness of the pre-trained models for biomedical entity normalization using three different types of datasets. Our experimental results show that the best fine-tuned models consistently outperformed previous methods and advanced the state-of-the-art for biomedical entity normalization, with up to 1.17% increase in accuracy.

Yuqi Si, Jingqi Wang, Hua Xu et al.

Neural network-based representations ("embeddings") have dramatically advanced natural language processing (NLP) tasks, including clinical NLP tasks such as concept extraction. Recently, however, more advanced embedding methods and representations (e.g., ELMo, BERT) have further pushed the state-of-the-art in NLP, yet there are no common best practices for how to integrate these representations into clinical tasks. The purpose of this study, then, is to explore the space of possible options in utilizing these new models for clinical concept extraction, including comparing these to traditional word embedding methods (word2vec, GloVe, fastText). Both off-the-shelf open-domain embeddings and pre-trained clinical embeddings from MIMIC-III are evaluated. We explore a battery of embedding methods consisting of traditional word embeddings and contextual embeddings, and compare these on four concept extraction corpora: i2b2 2010, i2b2 2012, SemEval 2014, and SemEval 2015. We also analyze the impact of the pre-training time of a large language model like ELMo or BERT on the extraction performance. Last, we present an intuitive way to understand the semantic information encoded by contextual embeddings. Contextual embeddings pre-trained on a large clinical corpus achieves new state-of-the-art performances across all concept extraction tasks. The best-performing model outperforms all state-of-the-art methods with respective F1-measures of 90.25, 93.18 (partial), 80.74, and 81.65. We demonstrate the potential of contextual embeddings through the state-of-the-art performance these methods achieve on clinical concept extraction. Additionally, we demonstrate contextual embeddings encode valuable semantic information not accounted for in traditional word representations.