arXiv subjects

Hongyi Yuan

Publications and source records attributed to Hongyi Yuan.

27 records · Page 2Linked to original sources

arXiv2023

SeqDiffuSeq: Text Diffusion with Encoder-Decoder Transformers

Diffusion model, a new generative modelling paradigm, has achieved great success in image, audio, and video generation. However, considering the discrete categorical nature of text, it is not trivial to extend continuous diffusion models to natural language, and text diffusion models are less studied. Sequence-to-sequence text generation is one of the essential natural language processing topics. In this work, we apply diffusion models to approach sequence-to-sequence text generation, and explore whether the superiority generation performance of diffusion model can transfer to natural language domain. We propose SeqDiffuSeq, a text diffusion model for sequence-to-sequence generation. SeqDiffuSeq uses an encoder-decoder Transformers architecture to model denoising function. In order to improve generation quality, SeqDiffuSeq combines the self-conditioning technique and a newly proposed adaptive noise schedule technique. The adaptive noise schedule has the difficulty of denoising evenly distributed across time steps, and considers exclusive noise schedules for tokens at different positional order. Experiment results illustrate the good performance on sequence-to-sequence generation in terms of text quality and inference time.

cs.CL↗

arXiv2023

HyPe: Better Pre-trained Language Model Fine-tuning with Hidden Representation Perturbation

Language models with the Transformers structure have shown great performance in natural language processing. However, there still poses problems when fine-tuning pre-trained language models on downstream tasks, such as over-fitting or representation collapse. In this work, we propose HyPe, a simple yet effective fine-tuning technique to alleviate such problems by perturbing hidden representations of Transformers layers. Unlike previous works that only add noise to inputs or parameters, we argue that the hidden representations of Transformers layers convey more diverse and meaningful language information. Therefore, making the Transformers layers more robust to hidden representation perturbations can further benefit the fine-tuning of PLMs en bloc. We conduct extensive experiments and analyses on GLUE and other natural language inference datasets. Results demonstrate that HyPe outperforms vanilla fine-tuning and enhances generalization of hidden representations from different layers. In addition, HyPe acquires negligible computational overheads, and is better than and compatible with previous state-of-the-art fine-tuning techniques.

cs.CL↗

arXiv2023

Revisiting Automatic Question Summarization Evaluation in the Biomedical Domain

Automatic evaluation metrics have been facilitating the rapid development of automatic summarization methods by providing instant and fair assessments of the quality of summaries. Most metrics have been developed for the general domain, especially news and meeting notes, or other language-generation tasks. However, these metrics are applied to evaluate summarization systems in different domains, such as biomedical question summarization. To better understand whether commonly used evaluation metrics are capable of evaluating automatic summarization in the biomedical domain, we conduct human evaluations of summarization quality from four different aspects of a biomedical question summarization task. Based on human judgments, we identify different noteworthy features for current automatic metrics and summarization systems as well. We also release a dataset of our human annotations to aid the research of summarization evaluation metrics in the biomedical domain.

cs.CL↗

arXiv2023

How well do Large Language Models perform in Arithmetic tasks?

Large language models have emerged abilities including chain-of-thought to answer math word problems step by step. Solving math word problems not only requires abilities to disassemble problems via chain-of-thought but also needs to calculate arithmetic expressions correctly for each step. To the best of our knowledge, there is no work to focus on evaluating the arithmetic ability of large language models. In this work, we propose an arithmetic dataset MATH 401 to test the latest large language models including GPT-4, ChatGPT, InstrctGPT, Galactica, and LLaMA with various arithmetic expressions and provide a detailed analysis of the ability of large language models. MATH 401 and evaluation codes are released at \url{https://github.com/GanjinZero/math401-llm}.

cs.CL↗

arXiv2023

RAMM: Retrieval-augmented Biomedical Visual Question Answering with Multi-modal Pre-training

Vision-and-language multi-modal pretraining and fine-tuning have shown great success in visual question answering (VQA). Compared to general domain VQA, the performance of biomedical VQA suffers from limited data. In this paper, we propose a retrieval-augmented pretrain-and-finetune paradigm named RAMM for biomedical VQA to overcome the data limitation issue. Specifically, we collect a new biomedical dataset named PMCPM which offers patient-based image-text pairs containing diverse patient situations from PubMed. Then, we pretrain the biomedical multi-modal model to learn visual and textual representation for image-text pairs and align these representations with image-text contrastive objective (ITC). Finally, we propose a retrieval-augmented method to better use the limited data. We propose to retrieve similar image-text pairs based on ITC from pretraining datasets and introduce a novel retrieval-attention module to fuse the representation of the image and the question with the retrieved images and texts. Experiments demonstrate that our retrieval-augmented pretrain-and-finetune paradigm obtains state-of-the-art performance on Med-VQA2019, Med-VQA2021, VQARAD, and SLAKE datasets. Further analysis shows that the proposed RAMM and PMCPM can enhance biomedical VQA performance compared with previous resources and methods. We will open-source our dataset, codes, and pretrained model.

cs.CV↗

arXiv2022

Efficient Symptom Inquiring and Diagnosis via Adaptive Alignment of Reinforcement Learning and Classification

Medical automatic diagnosis aims to imitate human doctors in real-world diagnostic processes and to achieve accurate diagnoses by interacting with the patients. The task is formulated as a sequential decision-making problem with a series of symptom inquiring steps and the final diagnosis. Recent research has studied incorporating reinforcement learning for symptom inquiring and classification techniques for disease diagnosis, respectively. However, studies on efficiently and effectively combining the two procedures are still lacking. To address this issue, we devise an adaptive mechanism to align reinforcement learning and classification methods using distribution entropy as the medium. Additionally, we created a new dataset for patient simulation to address the lacking of large-scale evaluation benchmarks. The dataset is extracted from the MedlinePlus knowledge base and contains significantly more diseases and more comprehensive symptoms and examination information than existing datasets. Experimental evaluation shows that our method outperforms three current state-of-the-art methods on different datasets by achieving higher medical diagnosis accuracy with fewer inquiring turns.

cs.LG↗

arXiv2022

Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning

Entities lie in the heart of biomedical natural language understanding, and the biomedical entity linking (EL) task remains challenging due to the fine-grained and diversiform concept names. Generative methods achieve remarkable performances in general domain EL with less memory usage while requiring expensive pre-training. Previous biomedical EL methods leverage synonyms from knowledge bases (KB) which is not trivial to inject into a generative method. In this work, we use a generative approach to model biomedical EL and propose to inject synonyms knowledge in it. We propose KB-guided pre-training by constructing synthetic samples with synonyms and definitions from KB and require the model to recover concept names. We also propose synonyms-aware fine-tuning to select concept names for training, and propose decoder prompt and multi-synonyms constrained prefix tree for inference. Our method achieves state-of-the-art results on several biomedical EL tasks without candidate selection which displays the effectiveness of proposed pre-training and fine-tuning strategies.

cs.CL↗

arXiv2022

BIOS: An Algorithmically Generated Biomedical Knowledge Graph

Biomedical knowledge graphs (BioMedKGs) are essential infrastructures for biomedical and healthcare big data and artificial intelligence (AI), facilitating natural language processing, model development, and data exchange. For decades, these knowledge graphs have been developed via expert curation; however, this method can no longer keep up with today's AI development, and a transition to algorithmically generated BioMedKGs is necessary. In this work, we introduce the Biomedical Informatics Ontology System (BIOS), the first large-scale publicly available BioMedKG generated completely by machine learning algorithms. BIOS currently contains 4.1 million concepts, 7.4 million terms in two languages, and 7.3 million relation triplets. We present the methodology for developing BIOS, including the curation of raw biomedical terms, computational identification of synonymous terms and aggregation of these terms to create concept nodes, semantic type classification of the concepts, relation identification, and biomedical machine translation. We provide statistics on the current BIOS content and perform preliminary assessments of term quality, synonym grouping, and relation extraction. The results suggest that machine learning-based BioMedKG development is a viable alternative to traditional expert curation.

cs.CL↗

arXiv2022

BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model

Pretrained language models have served as important backbones for natural language processing. Recently, in-domain pretraining has been shown to benefit various domain-specific downstream tasks. In the biomedical domain, natural language generation (NLG) tasks are of critical importance, while understudied. Approaching natural language understanding (NLU) tasks as NLG achieves satisfying performance in the general domain through constrained language generation or language prompting. We emphasize the lack of in-domain generative language models and the unsystematic generative downstream benchmarks in the biomedical domain, hindering the development of the research community. In this work, we introduce the generative language model BioBART that adapts BART to the biomedical domain. We collate various biomedical language generation tasks including dialogue, summarization, entity linking, and named entity recognition. BioBART pretrained on PubMed abstracts has enhanced performance compared to BART and set strong baselines on several tasks. Furthermore, we conduct ablation studies on the pretraining tasks for BioBART and find that sentence permutation has negative effects on downstream tasks.

cs.CL↗