arXiv subjects

Hua Xu

Publications and source records attributed to Hua Xu.

At least 91 records · Page 5Linked to original sources

arXiv2024

OpenVNA: A Framework for Analyzing the Behavior of Multimodal Language Understanding System under Noisy Scenarios

We present OpenVNA, an open-source framework designed for analyzing the behavior of multimodal language understanding systems under noisy conditions. OpenVNA serves as an intuitive toolkit tailored for researchers, facilitating convenience batch-level robustness evaluation and on-the-fly instance-level demonstration. It primarily features a benchmark Python library for assessing global model robustness, offering high flexibility and extensibility, thereby enabling customization with user-defined noise types and models. Additionally, a GUI-based interface has been developed to intuitively analyze local model behavior. In this paper, we delineate the design principles and utilization of the created library and GUI-based web platform. Currently, OpenVNA is publicly accessible at \url{https://github.com/thuiar/OpenVNA}, with a demonstration video available at \url{https://youtu.be/0Z9cW7RGct4}.

cs.MM↗

arXiv2024

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.

cs.MM↗

arXiv2024

Improving Entity Recognition Using Ensembles of Deep Learning and Fine-tuned Large Language Models: A Case Study on Adverse Event Extraction from Multiple Sources

Adverse event (AE) extraction following COVID-19 vaccines from text data is crucial for monitoring and analyzing the safety profiles of immunizations. Traditional deep learning models are adept at learning intricate feature representations and dependencies in sequential data, but often require extensive labeled data. In contrast, large language models (LLMs) excel in understanding contextual information, but exhibit unstable performance on named entity recognition tasks, possibly due to their broad but unspecific training. This study aims to evaluate the effectiveness of LLMs and traditional deep learning models in AE extraction, and to assess the impact of ensembling these models on performance. In this study, we utilized reports and posts from the VAERS (n=621), Twitter (n=9,133), and Reddit (n=131) as our corpora. Our goal was to extract three types of entities: "vaccine", "shot", and "ae". We explored and fine-tuned (except GPT-4) multiple LLMs, including GPT-2, GPT-3.5, GPT-4, and Llama-2, as well as traditional deep learning models like RNN and BioBERT. To enhance performance, we created ensembles of the three models with the best performance. For evaluation, we used strict and relaxed F1 scores to evaluate the performance for each entity type, and micro-average F1 was used to assess the overall performance. The ensemble model achieved the highest performance in "vaccine", "shot", and "ae" with strict F1-scores of 0.878, 0.930, and 0.925, respectively, along with a micro-average score of 0.903. In conclusion, this study demonstrates the effectiveness and robustness of ensembling fine-tuned traditional deep learning models and LLMs, for extracting AE-related information. This study contributes to the advancement of biomedical natural language processing, providing valuable insights into improving AE extraction from text data for pharmacovigilance and public health surveillance.

cs.CL↗

arXiv2024

Geneverse: A collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research

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.

cs.LG↗

arXiv2024

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.

cs.MM↗

arXiv2024

XL3M: A Training-free Framework for LLM Length Extension Based on Segment-wise Inference

Length generalization failure problem, namely the large language model (LLM) fails to generalize to texts longer than its maximum training length, greatly restricts the application of LLM in the scenarios with streaming long inputs. To address this problem, the existing methods either require substantial costs or introduce precision loss. In this paper, we empirically find that the accuracy of the LLM's prediction is highly correlated to its certainty. Based on this, we propose an efficient training free framework, named XL3M (it means extra-long large language model), which enables the LLMs trained on short sequences to reason extremely long sequence without any further training or fine-tuning. Under the XL3M framework, the input context will be firstly decomposed into multiple short sub-contexts, where each sub-context contains an independent segment and a common ``question'' which is a few tokens from the end of the original context. Then XL3M gives a method to measure the relevance between each segment and the ``question'', and constructs a concise key context by splicing all the relevant segments in chronological order. The key context is further used instead of the original context to complete the inference task. Evaluations on comprehensive benchmarks show the superiority of XL3M. Using our framework, a Llama2-7B model is able to reason 20M long sequences on an 8-card Huawei Ascend 910B NPU machine with 64GB memory per card.

cs.CL↗

arXiv2024

BiomedRAG: A Retrieval Augmented Large Language Model for Biomedicine

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.

cs.CL↗

arXiv2024

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.

cs.CL↗

arXiv2024

A Novel Quantum Algorithm for Ant Colony Optimization

Quantum ant colony optimization (QACO) has drew much attention since it combines the advantages of quantum computing and ant colony optimization (ACO) algorithms and overcomes some limitations of the traditional ACO algorithm. However, due to the hardware resource limitations of currently available quantum computers, such as the limited number of qubits, lack of high-fidelity gating operation, and low noisy tolerance, the practical application of the QACO is quite challenging. In this paper, we introduce a hybrid quantum-classical algorithm by combining the clustering algorithm with QACO algorithm, so that this extended QACO can handle large-scale optimization problems, which makes the practical application of QACO based on available quantum computation resource possible. To verify the effectiveness and performance of the algorithm, we tested the developed QACO algorithm with the Travelling Salesman Problem (TSP) as benchmarks. The developed QACO algorithm shows better performance under multiple data set. In addition, the developed QACO algorithm also manifests the robustness to noise of calculation process, which is typically a major barrier for practical application of quantum computers. Our work shows that the combination of the clustering algorithm with QACO has effectively extended the application scenario of QACO in current NISQ era of quantum computing.

quant-ph↗

arXiv2024

Improving Large Language Models for Clinical Named Entity Recognition via Prompt Engineering

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.

cs.CL↗

arXiv2024

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.

cs.IR↗

arXiv2023

A Clustering Framework for Unsupervised and Semi-supervised New Intent Discovery

New intent discovery is of great value to natural language processing, allowing for a better understanding of user needs and providing friendly services. However, most existing methods struggle to capture the complicated semantics of discrete text representations when limited or no prior knowledge of labeled data is available. To tackle this problem, we propose a novel clustering framework, USNID, for unsupervised and semi-supervised new intent discovery, which has three key technologies. First, it fully utilizes unsupervised or semi-supervised data to mine shallow semantic similarity relations and provide well-initialized representations for clustering. Second, it designs a centroid-guided clustering mechanism to address the issue of cluster allocation inconsistency and provide high-quality self-supervised targets for representation learning. Third, it captures high-level semantics in unsupervised or semi-supervised data to discover fine-grained intent-wise clusters by optimizing both cluster-level and instance-level objectives. We also propose an effective method for estimating the cluster number in open-world scenarios without knowing the number of new intents beforehand. USNID performs exceptionally well on several benchmark intent datasets, achieving new state-of-the-art results in unsupervised and semi-supervised new intent discovery and demonstrating robust performance with different cluster numbers.

cs.CL↗

arXiv2023

Ascle: A Python Natural Language Processing Toolkit for Medical Text Generation

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.

cs.CL↗

arXiv2023

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.

cs.CL↗

arXiv2023

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.

cs.CL↗

arXiv2023

Systematic Design and Evaluation of Social Determinants of Health Ontology (SDoHO)

Social determinants of health (SDoH) have a significant impact on health outcomes and well-being. Addressing SDoH is the key to reducing healthcare inequalities and transforming a "sick care" system into a "health promoting" system. To address the SDOH terminology gap and better embed relevant elements in advanced biomedical informatics, we propose an SDoH ontology (SDoHO), which represents fundamental SDoH factors and their relationships in a standardized and measurable way. The ontology formally models classes, relationships, and constraints based on multiple SDoH-related resources. Expert review and coverage evaluation, using clinical notes data and a national survey, showed satisfactory results. SDoHO could potentially play an essential role in providing a foundation for a comprehensive understanding of the associations between SDoH and health outcomes and providing a path toward health equity across populations.

cs.CY↗

arXiv2023

Learning Discriminative Representations and Decision Boundaries for Open Intent Detection

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.

cs.CL↗

arXiv2023

Controllable CVD-Growth of 2D Cr5Te8 Nanosheets with Thickness-Dependent Magnetic Domains

As a typical 2D magnetic material with self-intercalated structure, Cr5Te8 exhibits many fascinating magnetic properties. Although the ferromagnetism of 2D Cr5Te8 has been reported, the study of its magnetic domain is still blank. Herein, we successfully fabricated 2D Cr5Te8 nanosheets with controlled thickness and lateral size by chemical vapor deposition (CVD). Then magnetic property measurement system suggested Cr5Te8 nanosheets possessing intense out-of-plane ferromagnetism with the Curie temperature of 179 K. Most importantly, we found magnetic bubbles and thickness-dependent maze-like magnetic domains by cryogenic magnetic force microscopy (MFM) for the first time. The domain width of the maze-like magnetic domains increases rapidly with decreasing sample thickness, while domain contrast decreases. This indicates dipolar interaction is the dominant role over exchange interaction and magnetic anisotropy. Our work not only paves a way for the controllable growth of 2D magnetic materials, but also suggests new directions for controlling magnetic phases and systematically adjusting domain properties.

cond-mat.mes-hall↗