Relation Extraction Using Large Language Models: A Case Study on Acupuncture Point Locations

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.

MIntRec2.0: A Large-scale Benchmark Dataset for Multimodal Intent Recognition and Out-of-scope Detection in Conversations

Multimodal intent recognition poses significant challenges, requiring the incorporation of non-verbal modalities from real-world contexts to enhance the comprehension of human intentions. Existing benchmark datasets are limited in scale and suffer from difficulties in handling out-of-scope samples that arise in multi-turn conversational interactions. We introduce MIntRec2.0, a large-scale benchmark dataset for multimodal intent recognition in multi-party conversations. It contains 1,245 dialogues with 15,040 samples, each annotated within a new intent taxonomy of 30 fine-grained classes. Besides 9,304 in-scope samples, it also includes 5,736 out-of-scope samples appearing in multi-turn contexts, which naturally occur in real-world scenarios. Furthermore, we provide comprehensive information on the speakers in each utterance, enriching its utility for multi-party conversational research. We establish a general framework supporting the organization of single-turn and multi-turn dialogue data, modality feature extraction, multimodal fusion, as well as in-scope classification and out-of-scope detection. Evaluation benchmarks are built using classic multimodal fusion methods, ChatGPT, and human evaluators. While existing methods incorporating nonverbal information yield improvements, effectively leveraging context information and detecting out-of-scope samples remains a substantial challenge. Notably, large language models exhibit a significant performance gap compared to humans, highlighting the limitations of machine learning methods in the cognitive intent understanding task. We believe that MIntRec2.0 will serve as a valuable resource, providing a pioneering foundation for research in human-machine conversational interactions, and significantly facilitating related applications. The full dataset and codes are available at https://github.com/thuiar/MIntRec2.0.

Me LLaMA: Foundation Large Language Models for Medical Applications

Recent large language models (LLMs) like ChatGPT and LLaMA have shown great promise in many AI applications. However, their performance on medical tasks is suboptimal and can be further improved by training on large domain-specific datasets. This study introduces Me LLaMA, a medical LLM family including foundation models - Me LLaMA 13/70B and their chat-enhanced versions - Me LLaMA 13/70B-chat, developed through the continual pre-training and instruction tuning of LLaMA2 using large medical data. Our domain-specific data suite for training and evaluation, includes a large-scale continual pre-training dataset with 129B tokens, an instruction tuning dataset with 214k samples, and a medical evaluation benchmark (MIBE) across six tasks with 14 datasets. Our extensive evaluation using MIBE shows that Me LLaMA models surpass existing open-source medical LLMs in zero-shot and few-shot learning and outperform commercial giants like ChatGPT on 6 out of 8 datasets and GPT-4 in 3 out of 8 datasets. In addition, we empirically investigated the catastrophic forgetting problem, and our results show that Me LLaMA models outperform other medical LLMs. Me LLaMA is one of the first and largest open-source foundational LLMs designed for the medical domain, using both biomedical and clinical data. It exhibits superior performance across both general and medical tasks compared to other medical LLMs, rendering it an attractive choice for medical AI applications. All resources are available at: https://github.com/BIDS-Xu-Lab/Me-LLaMA.

A Span-based Model for Extracting Overlapping PICO Entities from RCT Publications

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.

Token-Level Contrastive Learning with Modality-Aware Prompting for Multimodal Intent Recognition

Multimodal intent recognition aims to leverage diverse modalities such as expressions, body movements and tone of speech to comprehend user's intent, constituting a critical task for understanding human language and behavior in real-world multimodal scenarios. Nevertheless, the majority of existing methods ignore potential correlations among different modalities and own limitations in effectively learning semantic features from nonverbal modalities. In this paper, we introduce a token-level contrastive learning method with modality-aware prompting (TCL-MAP) to address the above challenges. To establish an optimal multimodal semantic environment for text modality, we develop a modality-aware prompting module (MAP), which effectively aligns and fuses features from text, video and audio modalities with similarity-based modality alignment and cross-modality attention mechanism. Based on the modality-aware prompt and ground truth labels, the proposed token-level contrastive learning framework (TCL) constructs augmented samples and employs NT-Xent loss on the label token. Specifically, TCL capitalizes on the optimal textual semantic insights derived from intent labels to guide the learning processes of other modalities in return. Extensive experiments show that our method achieves remarkable improvements compared to state-of-the-art methods. Additionally, ablation analyses demonstrate the superiority of the modality-aware prompt over the handcrafted prompt, which holds substantial significance for multimodal prompt learning. The codes are released at https://github.com/thuiar/TCL-MAP.

MedGen: A Python Natural Language Processing Toolkit for Medical Text Processing

This study introduces MedGen, a comprehensive natural language processing (NLP) toolkit designed for medical text processing. MedGen is tailored for biomedical researchers and healthcare professionals with an easy-to-use, all-in-one solution that requires minimal programming expertise. It includes (1) Generative Functions: For the first time, MedGen includes four advanced generative functions: question answering, text summarization, text simplification, and machine translation; (2) Basic NLP Functions: MedGen integrates 12 essential NLP functions such as word tokenization and sentence segmentation; and (3) Query and Search Capabilities: MedGen provides user-friendly query and search functions on text corpora. We fine-tuned 32 domain-specific language models, evaluated them thoroughly on 24 established benchmarks and conducted manual reviews with clinicians. Additionally, we expanded our toolkit by introducing query and search functions, while also standardizing and integrating functions from third-party libraries. The toolkit, its models, and associated data are publicly available via https://github.com/Yale-LILY/MedGen.

AI Alignment: A Comprehensive Survey

AI alignment aims to make AI systems behave in line with human intentions and values. As AI systems grow more capable, the potential large-scale risks associated with misaligned AI systems become salient. Hundreds of AI experts and public figures have expressed concerns about AI risks, arguing that "mitigating the risk of extinction from AI should be a global priority, alongside other societal-scale risks such as pandemics and nuclear war". To provide a comprehensive and up-to-date overview of the alignment field, in this survey paper, we delve into the core concepts, methodology, and practice of alignment. We identify the RICE principles as the key objectives of AI alignment: Robustness, Interpretability, Controllability, and Ethicality. Guided by these four principles, we outline the landscape of current alignment research and decompose them into two key components: forward alignment and backward alignment. The former aims to make AI systems aligned via alignment training, while the latter aims to gain evidence about the systems' alignment and govern them appropriately to avoid exacerbating misalignment risks. Forward alignment and backward alignment form a recurrent process where the alignment of AI systems from the forward process is verified in the backward process, meanwhile providing updated objectives for forward alignment in the next round. On forward alignment, we discuss learning from feedback and learning under distribution shift. On backward alignment, we discuss assurance techniques and governance practices that apply to every stage of AI systems' lifecycle. We also release and continually update the website (www.alignmentsurvey.com) which features tutorials, collections of papers, blog posts, and other resources.

Identifying and Extracting Rare Disease Phenotypes with Large Language Models

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.

Complementary and Integrative Health Lexicon (CIHLex) and Entity Recognition in the Literature

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.