CLMar 20, 2023Code
DeID-GPT: Zero-shot Medical Text De-Identification by GPT-4Zhengliang Liu, Yue Huang, Xiaowei Yu et al.
The digitization of healthcare has facilitated the sharing and re-using of medical data but has also raised concerns about confidentiality and privacy. HIPAA (Health Insurance Portability and Accountability Act) mandates removing re-identifying information before the dissemination of medical records. Thus, effective and efficient solutions for de-identifying medical data, especially those in free-text forms, are highly needed. While various computer-assisted de-identification methods, including both rule-based and learning-based, have been developed and used in prior practice, such solutions still lack generalizability or need to be fine-tuned according to different scenarios, significantly imposing restrictions in wider use. The advancement of large language models (LLM), such as ChatGPT and GPT-4, have shown great potential in processing text data in the medical domain with zero-shot in-context learning, especially in the task of privacy protection, as these models can identify confidential information by their powerful named entity recognition (NER) capability. In this work, we developed a novel GPT4-enabled de-identification framework (``DeID-GPT") to automatically identify and remove the identifying information. Compared to existing commonly used medical text data de-identification methods, our developed DeID-GPT showed the highest accuracy and remarkable reliability in masking private information from the unstructured medical text while preserving the original structure and meaning of the text. This study is one of the earliest to utilize ChatGPT and GPT-4 for medical text data processing and de-identification, which provides insights for further research and solution development on the use of LLMs such as ChatGPT/GPT-4 in healthcare. Codes and benchmarking data information are available at https://github.com/yhydhx/ChatGPT-API.
CVSep 16, 2023Code
MA-SAM: Modality-agnostic SAM Adaptation for 3D Medical Image SegmentationCheng Chen, Juzheng Miao, Dufan Wu et al.
The Segment Anything Model (SAM), a foundation model for general image segmentation, has demonstrated impressive zero-shot performance across numerous natural image segmentation tasks. However, SAM's performance significantly declines when applied to medical images, primarily due to the substantial disparity between natural and medical image domains. To effectively adapt SAM to medical images, it is important to incorporate critical third-dimensional information, i.e., volumetric or temporal knowledge, during fine-tuning. Simultaneously, we aim to harness SAM's pre-trained weights within its original 2D backbone to the fullest extent. In this paper, we introduce a modality-agnostic SAM adaptation framework, named as MA-SAM, that is applicable to various volumetric and video medical data. Our method roots in the parameter-efficient fine-tuning strategy to update only a small portion of weight increments while preserving the majority of SAM's pre-trained weights. By injecting a series of 3D adapters into the transformer blocks of the image encoder, our method enables the pre-trained 2D backbone to extract third-dimensional information from input data. The effectiveness of our method has been comprehensively evaluated on four medical image segmentation tasks, by using 10 public datasets across CT, MRI, and surgical video data. Remarkably, without using any prompt, our method consistently outperforms various state-of-the-art 3D approaches, surpassing nnU-Net by 0.9%, 2.6%, and 9.9% in Dice for CT multi-organ segmentation, MRI prostate segmentation, and surgical scene segmentation respectively. Our model also demonstrates strong generalization, and excels in challenging tumor segmentation when prompts are used. Our code is available at: https://github.com/cchen-cc/MA-SAM.
CLJun 14, 2023Code
Radiology-GPT: A Large Language Model for RadiologyZhengliang Liu, Aoxiao Zhong, Yiwei Li et al.
We introduce Radiology-GPT, a large language model for radiology. Using an instruction tuning approach on an extensive dataset of radiology domain knowledge, Radiology-GPT demonstrates superior performance compared to general language models such as StableLM, Dolly and LLaMA. It exhibits significant versatility in radiological diagnosis, research, and communication. This work serves as a catalyst for future developments in clinical NLP. The successful implementation of Radiology-GPT is indicative of the potential of localizing generative large language models, specifically tailored for distinctive medical specialties, while ensuring adherence to privacy standards such as HIPAA. The prospect of developing individualized, large-scale language models that cater to specific needs of various hospitals presents a promising direction. The fusion of conversational competence and domain-specific knowledge in these models is set to foster future development in healthcare AI. A demo of Radiology-GPT is available at https://huggingface.co/spaces/allen-eric/radiology-gpt.
CVJul 3, 2023Code
SAMAug: Point Prompt Augmentation for Segment Anything ModelHaixing Dai, Chong Ma, Zhiling Yan et al.
This paper introduces SAMAug, a novel visual point augmentation method for the Segment Anything Model (SAM) that enhances interactive image segmentation performance. SAMAug generates augmented point prompts to provide more information about the user's intention to SAM. Starting with an initial point prompt, SAM produces an initial mask, which is then fed into our proposed SAMAug to generate augmented point prompts. By incorporating these extra points, SAM can generate augmented segmentation masks based on both the augmented point prompts and the initial prompt, resulting in improved segmentation performance. We conducted evaluations using four different point augmentation strategies: random sampling, sampling based on maximum difference entropy, maximum distance, and saliency. Experiment results on the COCO, Fundus, COVID QUEx, and ISIC2018 datasets show that SAMAug can boost SAM's segmentation results, especially using the maximum distance and saliency. SAMAug demonstrates the potential of visual prompt augmentation for computer vision. Codes of SAMAug are available at github.com/yhydhx/SAMAug
CLJun 16, 2023Code
AD-AutoGPT: An Autonomous GPT for Alzheimer's Disease InfodemiologyHaixing Dai, Yiwei Li, Zhengliang Liu et al.
In this pioneering study, inspired by AutoGPT, the state-of-the-art open-source application based on the GPT-4 large language model, we develop a novel tool called AD-AutoGPT which can conduct data collection, processing, and analysis about complex health narratives of Alzheimer's Disease in an autonomous manner via users' textual prompts. We collated comprehensive data from a variety of news sources, including the Alzheimer's Association, BBC, Mayo Clinic, and the National Institute on Aging since June 2022, leading to the autonomous execution of robust trend analyses, intertopic distance maps visualization, and identification of salient terms pertinent to Alzheimer's Disease. This approach has yielded not only a quantifiable metric of relevant discourse but also valuable insights into public focus on Alzheimer's Disease. This application of AD-AutoGPT in public health signifies the transformative potential of AI in facilitating a data-rich understanding of complex health narratives like Alzheimer's Disease in an autonomous manner, setting the groundwork for future AI-driven investigations in global health landscapes.
CLFeb 25, 2023
AugGPT: Leveraging ChatGPT for Text Data AugmentationHaixing Dai, Zhengliang Liu, Wenxiong Liao et al.
Text data augmentation is an effective strategy for overcoming the challenge of limited sample sizes in many natural language processing (NLP) tasks. This challenge is especially prominent in the few-shot learning scenario, where the data in the target domain is generally much scarcer and of lowered quality. A natural and widely-used strategy to mitigate such challenges is to perform data augmentation to better capture the data invariance and increase the sample size. However, current text data augmentation methods either can't ensure the correct labeling of the generated data (lacking faithfulness) or can't ensure sufficient diversity in the generated data (lacking compactness), or both. Inspired by the recent success of large language models, especially the development of ChatGPT, which demonstrated improved language comprehension abilities, in this work, we propose a text data augmentation approach based on ChatGPT (named AugGPT). AugGPT rephrases each sentence in the training samples into multiple conceptually similar but semantically different samples. The augmented samples can then be used in downstream model training. Experiment results on few-shot learning text classification tasks show the superior performance of the proposed AugGPT approach over state-of-the-art text data augmentation methods in terms of testing accuracy and distribution of the augmented samples.
85.0LGMay 28
World Models: A Comprehensive Survey of Architectures, Methodologies, Reasoning Paradigms, and ApplicationsArif Hassan Zidan, Yi Pan, Hanqi Jiang et al.
World models, internal simulators that learn the structure and dynamics of an environment, have emerged as a central paradigm in the pursuit of artificial general intelligence, enabling agents to predict, plan, and reason within learned representations. Despite rapid progress across reinforcement learning, robotics, autonomous driving, and video generation, the field lacks a unified framework integrating its diverse architectural choices, training methods, reasoning mechanisms, and application settings. This survey addresses that gap with a multi-axis taxonomy organized along four dimensions: (i) architecture, encompassing representation format, dynamics formulation, input modality, learning paradigm, and downstream application; (ii) methodological family, including state-space and recurrent approaches, transformer-based models, diffusion-based generators, physics-informed networks, and language-augmented multimodal systems; (iii) reasoning strategy, covering imagination-based planning, latent policy learning, counterfactual reasoning, and planning under uncertainty; and (iv) application domain, spanning robotics, autonomous driving, video prediction, multimodal agents, reinforcement learning, scientific modeling, medical imaging, educational measurement, and business and finance. Tracing the field from early cognitive-science foundations to milestone systems such as PlaNet, the Dreamer family, MuZero, Sora, Cosmos, and Genie, we examine how these dimensions interact and highlight the recent convergence of chain-of-thought reasoning with world-model imagination. We review evaluation protocols and benchmarks, identify persistent challenges such as compounding prediction errors, sim-to-real transfer, and fragmented evaluation, and outline future directions toward unified multimodal world models, foundation-scale interactive simulators, and safe deployment in safety-critical domains.
CLSep 27, 2023
MKRAG: Medical Knowledge Retrieval Augmented Generation for Medical Question AnsweringYucheng Shi, Shaochen Xu, Tianze Yang et al. · harvard
Large Language Models (LLMs), although powerful in general domains, often perform poorly on domain-specific tasks such as medical question answering (QA). In addition, LLMs tend to function as "black-boxes", making it challenging to modify their behavior. To address the problem, our work employs a transparent process of retrieval augmented generation (RAG), aiming to improve LLM responses without the need for fine-tuning or retraining. Specifically, we propose a comprehensive retrieval strategy to extract medical facts from an external knowledge base, and then inject them into the LLM's query prompt. Focusing on medical QA, we evaluate the impact of different retrieval models and the number of facts on LLM performance using the MedQA-SMILE dataset. Notably, our retrieval-augmented Vicuna-7B model exhibited an accuracy improvement from 44.46% to 48.54%. This work underscores the potential of RAG to enhance LLM performance, offering a practical approach to mitigate the challenges posed by black-box LLMs.
CLApr 4, 2023
Summary of ChatGPT-Related Research and Perspective Towards the Future of Large Language ModelsYiheng Liu, Tianle Han, Siyuan Ma et al.
This paper presents a comprehensive survey of ChatGPT-related (GPT-3.5 and GPT-4) research, state-of-the-art large language models (LLM) from the GPT series, and their prospective applications across diverse domains. Indeed, key innovations such as large-scale pre-training that captures knowledge across the entire world wide web, instruction fine-tuning and Reinforcement Learning from Human Feedback (RLHF) have played significant roles in enhancing LLMs' adaptability and performance. We performed an in-depth analysis of 194 relevant papers on arXiv, encompassing trend analysis, word cloud representation, and distribution analysis across various application domains. The findings reveal a significant and increasing interest in ChatGPT-related research, predominantly centered on direct natural language processing applications, while also demonstrating considerable potential in areas ranging from education and history to mathematics, medicine, and physics. This study endeavors to furnish insights into ChatGPT's capabilities, potential implications, ethical concerns, and offer direction for future advancements in this field.
MED-PHApr 1, 2023
Evaluating Large Language Models on a Highly-specialized Topic, Radiation Oncology PhysicsJason Holmes, Zhengliang Liu, Lian Zhang et al.
We present the first study to investigate Large Language Models (LLMs) in answering radiation oncology physics questions. Because popular exams like AP Physics, LSAT, and GRE have large test-taker populations and ample test preparation resources in circulation, they may not allow for accurately assessing the true potential of LLMs. This paper proposes evaluating LLMs on a highly-specialized topic, radiation oncology physics, which may be more pertinent to scientific and medical communities in addition to being a valuable benchmark of LLMs. We developed an exam consisting of 100 radiation oncology physics questions based on our expertise at Mayo Clinic. Four LLMs, ChatGPT (GPT-3.5), ChatGPT (GPT-4), Bard (LaMDA), and BLOOMZ, were evaluated against medical physicists and non-experts. ChatGPT (GPT-4) outperformed all other LLMs as well as medical physicists, on average. The performance of ChatGPT (GPT-4) was further improved when prompted to explain first, then answer. ChatGPT (GPT-3.5 and GPT-4) showed a high level of consistency in its answer choices across a number of trials, whether correct or incorrect, a characteristic that was not observed in the human test groups. In evaluating ChatGPTs (GPT-4) deductive reasoning ability using a novel approach (substituting the correct answer with "None of the above choices is the correct answer."), ChatGPT (GPT-4) demonstrated surprising accuracy, suggesting the potential presence of an emergent ability. Finally, although ChatGPT (GPT-4) performed well overall, its intrinsic properties did not allow for further improvement when scoring based on a majority vote across trials. In contrast, a team of medical physicists were able to greatly outperform ChatGPT (GPT-4) using a majority vote. This study suggests a great potential for LLMs to work alongside radiation oncology experts as highly knowledgeable assistants.
AINov 5, 2022
Coarse-to-fine Knowledge Graph Domain Adaptation based on Distantly-supervised Iterative TrainingHongmin Cai, Wenxiong Liao, Zhengliang Liu et al. · harvard
Modern supervised learning neural network models require a large amount of manually labeled data, which makes the construction of domain-specific knowledge graphs time-consuming and labor-intensive. In parallel, although there has been much research on named entity recognition and relation extraction based on distantly supervised learning, constructing a domain-specific knowledge graph from large collections of textual data without manual annotations is still an urgent problem to be solved. In response, we propose an integrated framework for adapting and re-learning knowledge graphs from one coarse domain (biomedical) to a finer-define domain (oncology). In this framework, we apply distant-supervision on cross-domain knowledge graph adaptation. Consequently, no manual data annotation is required to train the model. We introduce a novel iterative training strategy to facilitate the discovery of domain-specific named entities and triples. Experimental results indicate that the proposed framework can perform domain adaptation and construction of knowledge graph efficiently.
CVJul 3, 2023
Review of Large Vision Models and Visual Prompt EngineeringJiaqi Wang, Zhengliang Liu, Lin Zhao et al.
Visual prompt engineering is a fundamental technology in the field of visual and image Artificial General Intelligence, serving as a key component for achieving zero-shot capabilities. As the development of large vision models progresses, the importance of prompt engineering becomes increasingly evident. Designing suitable prompts for specific visual tasks has emerged as a meaningful research direction. This review aims to summarize the methods employed in the computer vision domain for large vision models and visual prompt engineering, exploring the latest advancements in visual prompt engineering. We present influential large models in the visual domain and a range of prompt engineering methods employed on these models. It is our hope that this review provides a comprehensive and systematic description of prompt engineering methods based on large visual models, offering valuable insights for future researchers in their exploration of this field.
CLAug 29, 2023
Radiology-Llama2: Best-in-Class Large Language Model for RadiologyZhengliang Liu, Yiwei Li, Peng Shu et al.
This paper introduces Radiology-Llama2, a large language model specialized for radiology through a process known as instruction tuning. Radiology-Llama2 is based on the Llama2 architecture and further trained on a large dataset of radiology reports to generate coherent and clinically useful impressions from radiological findings. Quantitative evaluations using ROUGE metrics on the MIMIC-CXR and OpenI datasets demonstrate that Radiology-Llama2 achieves state-of-the-art performance compared to other generative language models, with a Rouge-1 score of 0.4834 on MIMIC-CXR and 0.4185 on OpenI. Additional assessments by radiology experts highlight the model's strengths in understandability, coherence, relevance, conciseness, and clinical utility. The work illustrates the potential of localized language models designed and tuned for specialized domains like radiology. When properly evaluated and deployed, such models can transform fields like radiology by automating rote tasks and enhancing human expertise.
AIJun 8, 2023
Artificial General Intelligence for Medical Imaging AnalysisXiang Li, Lin Zhao, Lu Zhang et al.
Large-scale Artificial General Intelligence (AGI) models, including Large Language Models (LLMs) such as ChatGPT/GPT-4, have achieved unprecedented success in a variety of general domain tasks. Yet, when applied directly to specialized domains like medical imaging, which require in-depth expertise, these models face notable challenges arising from the medical field's inherent complexities and unique characteristics. In this review, we delve into the potential applications of AGI models in medical imaging and healthcare, with a primary focus on LLMs, Large Vision Models, and Large Multimodal Models. We provide a thorough overview of the key features and enabling techniques of LLMs and AGI, and further examine the roadmaps guiding the evolution and implementation of AGI models in the medical sector, summarizing their present applications, potentialities, and associated challenges. In addition, we highlight potential future research directions, offering a holistic view on upcoming ventures. This comprehensive review aims to offer insights into the future implications of AGI in medical imaging, healthcare, and beyond.
AIApr 28, 2023
Prompt Engineering for Healthcare: Methodologies and ApplicationsJiaqi Wang, Enze Shi, Sigang Yu et al.
Prompt engineering is a critical technique in the field of natural language processing that involves designing and optimizing the prompts used to input information into models, aiming to enhance their performance on specific tasks. With the recent advancements in large language models, prompt engineering has shown significant superiority across various domains and has become increasingly important in the healthcare domain. However, there is a lack of comprehensive reviews specifically focusing on prompt engineering in the medical field. This review will introduce the latest advances in prompt engineering in the field of natural language processing for the medical field. First, we will provide the development of prompt engineering and emphasize its significant contributions to healthcare natural language processing applications such as question-answering systems, text summarization, and machine translation. With the continuous improvement of general large language models, the importance of prompt engineering in the healthcare domain is becoming increasingly prominent. The aim of this article is to provide useful resources and bridges for healthcare natural language processing researchers to better explore the application of prompt engineering in this field. We hope that this review can provide new ideas and inspire for research and application in medical natural language processing.
CLApr 17, 2023
An Iterative Optimizing Framework for Radiology Report Summarization with ChatGPTChong Ma, Zihao Wu, Jiaqi Wang et al.
The 'Impression' section of a radiology report is a critical basis for communication between radiologists and other physicians, and it is typically written by radiologists based on the 'Findings' section. However, writing numerous impressions can be laborious and error-prone for radiologists. Although recent studies have achieved promising results in automatic impression generation using large-scale medical text data for pre-training and fine-tuning pre-trained language models, such models often require substantial amounts of medical text data and have poor generalization performance. While large language models (LLMs) like ChatGPT have shown strong generalization capabilities and performance, their performance in specific domains, such as radiology, remains under-investigated and potentially limited. To address this limitation, we propose ImpressionGPT, which leverages the in-context learning capability of LLMs by constructing dynamic contexts using domain-specific, individualized data. This dynamic prompt approach enables the model to learn contextual knowledge from semantically similar examples from existing data. Additionally, we design an iterative optimization algorithm that performs automatic evaluation on the generated impression results and composes the corresponding instruction prompts to further optimize the model. The proposed ImpressionGPT model achieves state-of-the-art performance on both MIMIC-CXR and OpenI datasets without requiring additional training data or fine-tuning the LLMs. This work presents a paradigm for localizing LLMs that can be applied in a wide range of similar application scenarios, bridging the gap between general-purpose LLMs and the specific language processing needs of various domains.
MED-PHSep 18, 2023
RadOnc-GPT: A Large Language Model for Radiation OncologyZhengliang Liu, Peilong Wang, Yiwei Li et al.
This paper presents RadOnc-GPT, a large language model specialized for radiation oncology through advanced tuning methods. RadOnc-GPT was finetuned on a large dataset of radiation oncology patient records from the Mayo Clinic in Arizona. The model employs instruction tuning on three key tasks - generating radiotherapy treatment regimens, determining optimal radiation modalities, and providing diagnostic descriptions/ICD codes based on patient diagnostic details. Evaluations conducted by comparing RadOnc-GPT outputs to general large language model outputs showed higher ROUGE scores in these three tasks. The study demonstrated the potential of using large language models fine-tuned using domain-specific knowledge like RadOnc-GPT to achieve transformational capabilities in highly specialized healthcare fields such as radiation oncology. However, our model's clinical relevance requires confirmation, and it specializes in only the aforementioned three specific tasks and lacks broader applicability. Furthermore, its evaluation through ROUGE scores might not reflect the true semantic and clinical accuracy - challenges we intend to address in future research.
IVJun 20, 2023
Segment Anything Model (SAM) for Radiation OncologyLian Zhang, Zhengliang Liu, Lu Zhang et al.
In this study, we evaluate the performance of the Segment Anything Model (SAM) in clinical radiotherapy. Our results indicate that SAM's 'segment anything' mode can achieve clinically acceptable segmentation results in most organs-at-risk (OARs) with Dice scores higher than 0.7. SAM's 'box prompt' mode further improves the Dice scores by 0.1 to 0.5. Considering the size of the organ and the clarity of its boundary, SAM displays better performance for large organs with clear boundaries but performs worse for smaller organs with unclear boundaries. Given that SAM, a model pre-trained purely on natural images, can handle the delineation of OARs from medical images with clinically acceptable accuracy, these results highlight SAM's robust generalization capabilities with consistent accuracy in automatic segmentation for radiotherapy. In other words, SAM can achieve delineation of different OARs at different sites using a generic automatic segmentation model. SAM's generalization capabilities across different disease sites suggest that it is technically feasible to develop a generic model for automatic segmentation in radiotherapy.
AIMar 28, 2023
When Brain-inspired AI Meets AGILin Zhao, Lu Zhang, Zihao Wu et al.
Artificial General Intelligence (AGI) has been a long-standing goal of humanity, with the aim of creating machines capable of performing any intellectual task that humans can do. To achieve this, AGI researchers draw inspiration from the human brain and seek to replicate its principles in intelligent machines. Brain-inspired artificial intelligence is a field that has emerged from this endeavor, combining insights from neuroscience, psychology, and computer science to develop more efficient and powerful AI systems. In this article, we provide a comprehensive overview of brain-inspired AI from the perspective of AGI. We begin with the current progress in brain-inspired AI and its extensive connection with AGI. We then cover the important characteristics for both human intelligence and AGI (e.g., scaling, multimodality, and reasoning). We discuss important technologies toward achieving AGI in current AI systems, such as in-context learning and prompt tuning. We also investigate the evolution of AGI systems from both algorithmic and infrastructural perspectives. Finally, we explore the limitations and future of AGI.
CVApr 21, 2023
Deep-Learning-based Fast and Accurate 3D CT Deformable Image Registration in Lung CancerYuzhen Ding, Hongying Feng, Yunze Yang et al.
Purpose: In some proton therapy facilities, patient alignment relies on two 2D orthogonal kV images, taken at fixed, oblique angles, as no 3D on-the-bed imaging is available. The visibility of the tumor in kV images is limited since the patient's 3D anatomy is projected onto a 2D plane, especially when the tumor is behind high-density structures such as bones. This can lead to large patient setup errors. A solution is to reconstruct the 3D CT image from the kV images obtained at the treatment isocenter in the treatment position. Methods: An asymmetric autoencoder-like network built with vision-transformer blocks was developed. The data was collected from 1 head and neck patient: 2 orthogonal kV images (1024x1024 voxels), 1 3D CT with padding (512x512x512) acquired from the in-room CT-on-rails before kVs were taken and 2 digitally-reconstructed-radiograph (DRR) images (512x512) based on the CT. We resampled kV images every 8 voxels and DRR and CT every 4 voxels, thus formed a dataset consisting of 262,144 samples, in which the images have a dimension of 128 for each direction. In training, both kV and DRR images were utilized, and the encoder was encouraged to learn the jointed feature map from both kV and DRR images. In testing, only independent kV images were used. The full-size synthetic CT (sCT) was achieved by concatenating the sCTs generated by the model according to their spatial information. The image quality of the synthetic CT (sCT) was evaluated using mean absolute error (MAE) and per-voxel-absolute-CT-number-difference volume histogram (CDVH). Results: The model achieved a speed of 2.1s and a MAE of <40HU. The CDVH showed that <5% of the voxels had a per-voxel-absolute-CT-number-difference larger than 185 HU. Conclusion: A patient-specific vision-transformer-based network was developed and shown to be accurate and efficient to reconstruct 3D CT images from kV images.
CLSep 19, 2023
PolicyGPT: Automated Analysis of Privacy Policies with Large Language ModelsChenhao Tang, Zhengliang Liu, Chong Ma et al.
Privacy policies serve as the primary conduit through which online service providers inform users about their data collection and usage procedures. However, in a bid to be comprehensive and mitigate legal risks, these policy documents are often quite verbose. In practical use, users tend to click the Agree button directly rather than reading them carefully. This practice exposes users to risks of privacy leakage and legal issues. Recently, the advent of Large Language Models (LLM) such as ChatGPT and GPT-4 has opened new possibilities for text analysis, especially for lengthy documents like privacy policies. In this study, we investigate a privacy policy text analysis framework PolicyGPT based on the LLM. This framework was tested using two datasets. The first dataset comprises of privacy policies from 115 websites, which were meticulously annotated by legal experts, categorizing each segment into one of 10 classes. The second dataset consists of privacy policies from 304 popular mobile applications, with each sentence manually annotated and classified into one of another 10 categories. Under zero-shot learning conditions, PolicyGPT demonstrated robust performance. For the first dataset, it achieved an accuracy rate of 97%, while for the second dataset, it attained an 87% accuracy rate, surpassing that of the baseline machine learning and neural network models.
CLJul 25, 2023
Evaluating Large Language Models for Radiology Natural Language ProcessingZhengliang Liu, Tianyang Zhong, Yiwei Li et al.
The rise of large language models (LLMs) has marked a pivotal shift in the field of natural language processing (NLP). LLMs have revolutionized a multitude of domains, and they have made a significant impact in the medical field. Large language models are now more abundant than ever, and many of these models exhibit bilingual capabilities, proficient in both English and Chinese. However, a comprehensive evaluation of these models remains to be conducted. This lack of assessment is especially apparent within the context of radiology NLP. This study seeks to bridge this gap by critically evaluating thirty two LLMs in interpreting radiology reports, a crucial component of radiology NLP. Specifically, the ability to derive impressions from radiologic findings is assessed. The outcomes of this evaluation provide key insights into the performance, strengths, and weaknesses of these LLMs, informing their practical applications within the medical domain.
CLApr 23, 2023
Differentiate ChatGPT-generated and Human-written Medical TextsWenxiong Liao, Zhengliang Liu, Haixing Dai et al.
Background: Large language models such as ChatGPT are capable of generating grammatically perfect and human-like text content, and a large number of ChatGPT-generated texts have appeared on the Internet. However, medical texts such as clinical notes and diagnoses require rigorous validation, and erroneous medical content generated by ChatGPT could potentially lead to disinformation that poses significant harm to healthcare and the general public. Objective: This research is among the first studies on responsible and ethical AIGC (Artificial Intelligence Generated Content) in medicine. We focus on analyzing the differences between medical texts written by human experts and generated by ChatGPT, and designing machine learning workflows to effectively detect and differentiate medical texts generated by ChatGPT. Methods: We first construct a suite of datasets containing medical texts written by human experts and generated by ChatGPT. In the next step, we analyze the linguistic features of these two types of content and uncover differences in vocabulary, part-of-speech, dependency, sentiment, perplexity, etc. Finally, we design and implement machine learning methods to detect medical text generated by ChatGPT. Results: Medical texts written by humans are more concrete, more diverse, and typically contain more useful information, while medical texts generated by ChatGPT pay more attention to fluency and logic, and usually express general terminologies rather than effective information specific to the context of the problem. A BERT-based model can effectively detect medical texts generated by ChatGPT, and the F1 exceeds 95%.
CLApr 18, 2023
Exploring the Trade-Offs: Unified Large Language Models vs Local Fine-Tuned Models for Highly-Specific Radiology NLI TaskZihao Wu, Lu Zhang, Chao Cao et al.
Recently, ChatGPT and GPT-4 have emerged and gained immense global attention due to their unparalleled performance in language processing. Despite demonstrating impressive capability in various open-domain tasks, their adequacy in highly specific fields like radiology remains untested. Radiology presents unique linguistic phenomena distinct from open-domain data due to its specificity and complexity. Assessing the performance of large language models (LLMs) in such specific domains is crucial not only for a thorough evaluation of their overall performance but also for providing valuable insights into future model design directions: whether model design should be generic or domain-specific. To this end, in this study, we evaluate the performance of ChatGPT/GPT-4 on a radiology NLI task and compare it to other models fine-tuned specifically on task-related data samples. We also conduct a comprehensive investigation on ChatGPT/GPT-4's reasoning ability by introducing varying levels of inference difficulty. Our results show that 1) GPT-4 outperforms ChatGPT in the radiology NLI task; 2) other specifically fine-tuned models require significant amounts of data samples to achieve comparable performance to ChatGPT/GPT-4. These findings demonstrate that constructing a generic model that is capable of solving various tasks across different domains is feasible.
CLFeb 21, 2023
Mask-guided BERT for Few Shot Text ClassificationWenxiong Liao, Zhengliang Liu, Haixing Dai et al.
Transformer-based language models have achieved significant success in various domains. However, the data-intensive nature of the transformer architecture requires much labeled data, which is challenging in low-resource scenarios (i.e., few-shot learning (FSL)). The main challenge of FSL is the difficulty of training robust models on small amounts of samples, which frequently leads to overfitting. Here we present Mask-BERT, a simple and modular framework to help BERT-based architectures tackle FSL. The proposed approach fundamentally differs from existing FSL strategies such as prompt tuning and meta-learning. The core idea is to selectively apply masks on text inputs and filter out irrelevant information, which guides the model to focus on discriminative tokens that influence prediction results. In addition, to make the text representations from different categories more separable and the text representations from the same category more compact, we introduce a contrastive learning loss function. Experimental results on public-domain benchmark datasets demonstrate the effectiveness of Mask-BERT.
CLJun 20, 2023
Exploring New Frontiers in Agricultural NLP: Investigating the Potential of Large Language Models for Food ApplicationsSaed Rezayi, Zhengliang Liu, Zihao Wu et al.
This paper explores new frontiers in agricultural natural language processing by investigating the effectiveness of using food-related text corpora for pretraining transformer-based language models. In particular, we focus on the task of semantic matching, which involves establishing mappings between food descriptions and nutrition data. To accomplish this, we fine-tune a pre-trained transformer-based language model, AgriBERT, on this task, utilizing an external source of knowledge, such as the FoodOn ontology. To advance the field of agricultural NLP, we propose two new avenues of exploration: (1) utilizing GPT-based models as a baseline and (2) leveraging ChatGPT as an external source of knowledge. ChatGPT has shown to be a strong baseline in many NLP tasks, and we believe it has the potential to improve our model in the task of semantic matching and enhance our model's understanding of food-related concepts and relationships. Additionally, we experiment with other applications, such as cuisine prediction based on food ingredients, and expand the scope of our research to include other NLP tasks beyond semantic matching. Overall, this paper provides promising avenues for future research in this field, with potential implications for improving the performance of agricultural NLP applications.
CVMay 25, 2022
Eye-gaze-guided Vision Transformer for Rectifying Shortcut LearningChong Ma, Lin Zhao, Yuzhong Chen et al.
Learning harmful shortcuts such as spurious correlations and biases prevents deep neural networks from learning the meaningful and useful representations, thus jeopardizing the generalizability and interpretability of the learned representation. The situation becomes even more serious in medical imaging, where the clinical data (e.g., MR images with pathology) are limited and scarce while the reliability, generalizability and transparency of the learned model are highly required. To address this problem, we propose to infuse human experts' intelligence and domain knowledge into the training of deep neural networks. The core idea is that we infuse the visual attention information from expert radiologists to proactively guide the deep model to focus on regions with potential pathology and avoid being trapped in learning harmful shortcuts. To do so, we propose a novel eye-gaze-guided vision transformer (EG-ViT) for diagnosis with limited medical image data. We mask the input image patches that are out of the radiologists' interest and add an additional residual connection in the last encoder layer of EG-ViT to maintain the correlations of all patches. The experiments on two public datasets of INbreast and SIIM-ACR demonstrate our EG-ViT model can effectively learn/transfer experts' domain knowledge and achieve much better performance than baselines. Meanwhile, it successfully rectifies the harmful shortcut learning and significantly improves the EG-ViT model's interpretability. In general, EG-ViT takes the advantages of both human expert's prior knowledge and the power of deep neural networks. This work opens new avenues for advancing current artificial intelligence paradigms by infusing human intelligence.
CLSep 27, 2024
Evaluation of OpenAI o1: Opportunities and Challenges of AGITianyang Zhong, Zhengliang Liu, Yi Pan et al.
This comprehensive study evaluates the performance of OpenAI's o1-preview large language model across a diverse array of complex reasoning tasks, spanning multiple domains, including computer science, mathematics, natural sciences, medicine, linguistics, and social sciences. Through rigorous testing, o1-preview demonstrated remarkable capabilities, often achieving human-level or superior performance in areas ranging from coding challenges to scientific reasoning and from language processing to creative problem-solving. Key findings include: -83.3% success rate in solving complex competitive programming problems, surpassing many human experts. -Superior ability in generating coherent and accurate radiology reports, outperforming other evaluated models. -100% accuracy in high school-level mathematical reasoning tasks, providing detailed step-by-step solutions. -Advanced natural language inference capabilities across general and specialized domains like medicine. -Impressive performance in chip design tasks, outperforming specialized models in areas such as EDA script generation and bug analysis. -Remarkable proficiency in anthropology and geology, demonstrating deep understanding and reasoning in these specialized fields. -Strong capabilities in quantitative investing. O1 has comprehensive financial knowledge and statistical modeling skills. -Effective performance in social media analysis, including sentiment analysis and emotion recognition. The model excelled particularly in tasks requiring intricate reasoning and knowledge integration across various fields. While some limitations were observed, including occasional errors on simpler problems and challenges with certain highly specialized concepts, the overall results indicate significant progress towards artificial general intelligence.
AISep 14, 2023
Towards Artificial General Intelligence (AGI) in the Internet of Things (IoT): Opportunities and ChallengesFei Dou, Jin Ye, Geng Yuan et al.
Artificial General Intelligence (AGI), possessing the capacity to comprehend, learn, and execute tasks with human cognitive abilities, engenders significant anticipation and intrigue across scientific, commercial, and societal arenas. This fascination extends particularly to the Internet of Things (IoT), a landscape characterized by the interconnection of countless devices, sensors, and systems, collectively gathering and sharing data to enable intelligent decision-making and automation. This research embarks on an exploration of the opportunities and challenges towards achieving AGI in the context of the IoT. Specifically, it starts by outlining the fundamental principles of IoT and the critical role of Artificial Intelligence (AI) in IoT systems. Subsequently, it delves into AGI fundamentals, culminating in the formulation of a conceptual framework for AGI's seamless integration within IoT. The application spectrum for AGI-infused IoT is broad, encompassing domains ranging from smart grids, residential environments, manufacturing, and transportation to environmental monitoring, agriculture, healthcare, and education. However, adapting AGI to resource-constrained IoT settings necessitates dedicated research efforts. Furthermore, the paper addresses constraints imposed by limited computing resources, intricacies associated with large-scale IoT communication, as well as the critical concerns pertaining to security and privacy.
CLApr 21, 2023
ChatABL: Abductive Learning via Natural Language Interaction with ChatGPTTianyang Zhong, Yaonai Wei, Li Yang et al.
Large language models (LLMs) such as ChatGPT have recently demonstrated significant potential in mathematical abilities, providing valuable reasoning paradigm consistent with human natural language. However, LLMs currently have difficulty in bridging perception, language understanding and reasoning capabilities due to incompatibility of the underlying information flow among them, making it challenging to accomplish tasks autonomously. On the other hand, abductive learning (ABL) frameworks for integrating the two abilities of perception and reasoning has seen significant success in inverse decipherment of incomplete facts, but it is limited by the lack of semantic understanding of logical reasoning rules and the dependence on complicated domain knowledge representation. This paper presents a novel method (ChatABL) for integrating LLMs into the ABL framework, aiming at unifying the three abilities in a more user-friendly and understandable manner. The proposed method uses the strengths of LLMs' understanding and logical reasoning to correct the incomplete logical facts for optimizing the performance of perceptual module, by summarizing and reorganizing reasoning rules represented in natural language format. Similarly, perceptual module provides necessary reasoning examples for LLMs in natural language format. The variable-length handwritten equation deciphering task, an abstract expression of the Mayan calendar decoding, is used as a testbed to demonstrate that ChatABL has reasoning ability beyond most existing state-of-the-art methods, which has been well supported by comparative studies. To our best knowledge, the proposed ChatABL is the first attempt to explore a new pattern for further approaching human-level cognitive ability via natural language interaction with ChatGPT.
CLJan 23Code
Large Language Models for Assisting American College ApplicationsZhengliang Liu, Weihang You, Peng Shu et al.
American college applications require students to navigate fragmented admissions policies, repetitive and conditional forms, and ambiguous questions that often demand cross-referencing multiple sources. We present EZCollegeApp, a large language model (LLM)-powered system that assists high-school students by structuring application forms, grounding suggested answers in authoritative admissions documents, and maintaining full human control over final responses. The system introduces a mapping-first paradigm that separates form understanding from answer generation, enabling consistent reasoning across heterogeneous application portals. EZCollegeApp integrates document ingestion from official admissions websites, retrieval-augmented question answering, and a human-in-the-loop chatbot interface that presents suggestions alongside application fields without automated submission. We describe the system architecture, data pipeline, internal representations, security and privacy measures, and evaluation through automated testing and human quality assessment. Our source code is released on GitHub (https://github.com/ezcollegeapp-public/ezcollegeapp-public) to facilitate the broader impact of this work.
AIAug 2, 2024
A Comprehensive Review of Multimodal Large Language Models: Performance and Challenges Across Different TasksJiaqi Wang, Hanqi Jiang, Yiheng Liu et al.
In an era defined by the explosive growth of data and rapid technological advancements, Multimodal Large Language Models (MLLMs) stand at the forefront of artificial intelligence (AI) systems. Designed to seamlessly integrate diverse data types-including text, images, videos, audio, and physiological sequences-MLLMs address the complexities of real-world applications far beyond the capabilities of single-modality systems. In this paper, we systematically sort out the applications of MLLM in multimodal tasks such as natural language, vision, and audio. We also provide a comparative analysis of the focus of different MLLMs in the tasks, and provide insights into the shortcomings of current MLLMs, and suggest potential directions for future research. Through these discussions, this paper hopes to provide valuable insights for the further development and application of MLLM.
ASJul 5, 2023
Exploring Multimodal Approaches for Alzheimer's Disease Detection Using Patient Speech Transcript and Audio DataHongmin Cai, Xiaoke Huang, Zhengliang Liu et al.
Alzheimer's disease (AD) is a common form of dementia that severely impacts patient health. As AD impairs the patient's language understanding and expression ability, the speech of AD patients can serve as an indicator of this disease. This study investigates various methods for detecting AD using patients' speech and transcripts data from the DementiaBank Pitt database. The proposed approach involves pre-trained language models and Graph Neural Network (GNN) that constructs a graph from the speech transcript, and extracts features using GNN for AD detection. Data augmentation techniques, including synonym replacement, GPT-based augmenter, and so on, were used to address the small dataset size. Audio data was also introduced, and WavLM model was used to extract audio features. These features were then fused with text features using various methods. Finally, a contrastive learning approach was attempted by converting speech transcripts back to audio and using it for contrastive learning with the original audio. We conducted intensive experiments and analysis on the above methods. Our findings shed light on the challenges and potential solutions in AD detection using speech and audio data.
CLJul 21, 2023
CohortGPT: An Enhanced GPT for Participant Recruitment in Clinical StudyZihan Guan, Zihao Wu, Zhengliang Liu et al.
Participant recruitment based on unstructured medical texts such as clinical notes and radiology reports has been a challenging yet important task for the cohort establishment in clinical research. Recently, Large Language Models (LLMs) such as ChatGPT have achieved tremendous success in various downstream tasks thanks to their promising performance in language understanding, inference, and generation. It is then natural to test their feasibility in solving the cohort recruitment task, which involves the classification of a given paragraph of medical text into disease label(s). However, when applied to knowledge-intensive problem settings such as medical text classification, where the LLMs are expected to understand the decision made by human experts and accurately identify the implied disease labels, the LLMs show a mediocre performance. A possible explanation is that, by only using the medical text, the LLMs neglect to use the rich context of additional information that languages afford. To this end, we propose to use a knowledge graph as auxiliary information to guide the LLMs in making predictions. Moreover, to further boost the LLMs adapt to the problem setting, we apply a chain-of-thought (CoT) sample selection strategy enhanced by reinforcement learning, which selects a set of CoT samples given each individual medical report. Experimental results and various ablation studies show that our few-shot learning method achieves satisfactory performance compared with fine-tuning strategies and gains superb advantages when the available data is limited. The code and sample dataset of the proposed CohortGPT model is available at: https://anonymous.4open.science/r/CohortGPT-4872/
CLSep 10, 2023
Chat2Brain: A Method for Mapping Open-Ended Semantic Queries to Brain Activation MapsYaonai Wei, Tuo Zhang, Han Zhang et al.
Over decades, neuroscience has accumulated a wealth of research results in the text modality that can be used to explore cognitive processes. Meta-analysis is a typical method that successfully establishes a link from text queries to brain activation maps using these research results, but it still relies on an ideal query environment. In practical applications, text queries used for meta-analyses may encounter issues such as semantic redundancy and ambiguity, resulting in an inaccurate mapping to brain images. On the other hand, large language models (LLMs) like ChatGPT have shown great potential in tasks such as context understanding and reasoning, displaying a high degree of consistency with human natural language. Hence, LLMs could improve the connection between text modality and neuroscience, resolving existing challenges of meta-analyses. In this study, we propose a method called Chat2Brain that combines LLMs to basic text-2-image model, known as Text2Brain, to map open-ended semantic queries to brain activation maps in data-scarce and complex query environments. By utilizing the understanding and reasoning capabilities of LLMs, the performance of the mapping model is optimized by transferring text queries to semantic queries. We demonstrate that Chat2Brain can synthesize anatomically plausible neural activation patterns for more complex tasks of text queries.
CVMay 19, 2022
Discovering Dynamic Functional Brain Networks via Spatial and Channel-wise AttentionYiheng Liu, Enjie Ge, Mengshen He et al.
Using deep learning models to recognize functional brain networks (FBNs) in functional magnetic resonance imaging (fMRI) has been attracting increasing interest recently. However, most existing work focuses on detecting static FBNs from entire fMRI signals, such as correlation-based functional connectivity. Sliding-window is a widely used strategy to capture the dynamics of FBNs, but it is still limited in representing intrinsic functional interactive dynamics at each time step. And the number of FBNs usually need to be set manually. More over, due to the complexity of dynamic interactions in brain, traditional linear and shallow models are insufficient in identifying complex and spatially overlapped FBNs across each time step. In this paper, we propose a novel Spatial and Channel-wise Attention Autoencoder (SCAAE) for discovering FBNs dynamically. The core idea of SCAAE is to apply attention mechanism to FBNs construction. Specifically, we designed two attention modules: 1) spatial-wise attention (SA) module to discover FBNs in the spatial domain and 2) a channel-wise attention (CA) module to weigh the channels for selecting the FBNs automatically. We evaluated our approach on ADHD200 dataset and our results indicate that the proposed SCAAE method can effectively recover the dynamic changes of the FBNs at each fMRI time step, without using sliding windows. More importantly, our proposed hybrid attention modules (SA and CA) do not enforce assumptions of linearity and independence as previous methods, and thus provide a novel approach to better understanding dynamic functional brain networks.
CLOct 8, 2023
ChatRadio-Valuer: A Chat Large Language Model for Generalizable Radiology Report Generation Based on Multi-institution and Multi-system DataTianyang Zhong, Wei Zhao, Yutong Zhang et al.
Radiology report generation, as a key step in medical image analysis, is critical to the quantitative analysis of clinically informed decision-making levels. However, complex and diverse radiology reports with cross-source heterogeneity pose a huge generalizability challenge to the current methods under massive data volume, mainly because the style and normativity of radiology reports are obviously distinctive among institutions, body regions inspected and radiologists. Recently, the advent of large language models (LLM) offers great potential for recognizing signs of health conditions. To resolve the above problem, we collaborate with the Second Xiangya Hospital in China and propose ChatRadio-Valuer based on the LLM, a tailored model for automatic radiology report generation that learns generalizable representations and provides a basis pattern for model adaptation in sophisticated analysts' cases. Specifically, ChatRadio-Valuer is trained based on the radiology reports from a single institution by means of supervised fine-tuning, and then adapted to disease diagnosis tasks for human multi-system evaluation (i.e., chest, abdomen, muscle-skeleton, head, and maxillofacial $\&$ neck) from six different institutions in clinical-level events. The clinical dataset utilized in this study encompasses a remarkable total of \textbf{332,673} observations. From the comprehensive results on engineering indicators, clinical efficacy and deployment cost metrics, it can be shown that ChatRadio-Valuer consistently outperforms state-of-the-art models, especially ChatGPT (GPT-3.5-Turbo) and GPT-4 et al., in terms of the diseases diagnosis from radiology reports. ChatRadio-Valuer provides an effective avenue to boost model generalization performance and alleviate the annotation workload of experts to enable the promotion of clinical AI applications in radiology reports.
IVNov 10, 2023
Holistic Evaluation of GPT-4V for Biomedical ImagingZhengliang Liu, Hanqi Jiang, Tianyang Zhong et al.
In this paper, we present a large-scale evaluation probing GPT-4V's capabilities and limitations for biomedical image analysis. GPT-4V represents a breakthrough in artificial general intelligence (AGI) for computer vision, with applications in the biomedical domain. We assess GPT-4V's performance across 16 medical imaging categories, including radiology, oncology, ophthalmology, pathology, and more. Tasks include modality recognition, anatomy localization, disease diagnosis, report generation, and lesion detection. The extensive experiments provide insights into GPT-4V's strengths and weaknesses. Results show GPT-4V's proficiency in modality and anatomy recognition but difficulty with disease diagnosis and localization. GPT-4V excels at diagnostic report generation, indicating strong image captioning skills. While promising for biomedical imaging AI, GPT-4V requires further enhancement and validation before clinical deployment. We emphasize responsible development and testing for trustworthy integration of biomedical AGI. This rigorous evaluation of GPT-4V on diverse medical images advances understanding of multimodal large language models (LLMs) and guides future work toward impactful healthcare applications.
CVJul 10, 2023
Hierarchical Semantic Tree Concept Whitening for Interpretable Image ClassificationHaixing Dai, Lu Zhang, Lin Zhao et al.
With the popularity of deep neural networks (DNNs), model interpretability is becoming a critical concern. Many approaches have been developed to tackle the problem through post-hoc analysis, such as explaining how predictions are made or understanding the meaning of neurons in middle layers. Nevertheless, these methods can only discover the patterns or rules that naturally exist in models. In this work, rather than relying on post-hoc schemes, we proactively instill knowledge to alter the representation of human-understandable concepts in hidden layers. Specifically, we use a hierarchical tree of semantic concepts to store the knowledge, which is leveraged to regularize the representations of image data instances while training deep models. The axes of the latent space are aligned with the semantic concepts, where the hierarchical relations between concepts are also preserved. Experiments on real-world image datasets show that our method improves model interpretability, showing better disentanglement of semantic concepts, without negatively affecting model classification performance.
AIOct 30, 2023
Transformation vs Tradition: Artificial General Intelligence (AGI) for Arts and HumanitiesZhengliang Liu, Yiwei Li, Qian Cao et al.
Recent advances in artificial general intelligence (AGI), particularly large language models and creative image generation systems have demonstrated impressive capabilities on diverse tasks spanning the arts and humanities. However, the swift evolution of AGI has also raised critical questions about its responsible deployment in these culturally significant domains traditionally seen as profoundly human. This paper provides a comprehensive analysis of the applications and implications of AGI for text, graphics, audio, and video pertaining to arts and the humanities. We survey cutting-edge systems and their usage in areas ranging from poetry to history, marketing to film, and communication to classical art. We outline substantial concerns pertaining to factuality, toxicity, biases, and public safety in AGI systems, and propose mitigation strategies. The paper argues for multi-stakeholder collaboration to ensure AGI promotes creativity, knowledge, and cultural values without undermining truth or human dignity. Our timely contribution summarizes a rapidly developing field, highlighting promising directions while advocating for responsible progress centering on human flourishing. The analysis lays the groundwork for further research on aligning AGI's technological capacities with enduring social goods.
CLSep 15, 2024
GP-GPT: Large Language Model for Gene-Phenotype MappingYanjun Lyu, Zihao Wu, Lu Zhang et al.
Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.
AIJan 27, 2023
Context Matters: A Strategy to Pre-train Language Model for Science EducationZhengliang Liu, Xinyu He, Lei Liu et al.
This study aims at improving the performance of scoring student responses in science education automatically. BERT-based language models have shown significant superiority over traditional NLP models in various language-related tasks. However, science writing of students, including argumentation and explanation, is domain-specific. In addition, the language used by students is different from the language in journals and Wikipedia, which are training sources of BERT and its existing variants. All these suggest that a domain-specific model pre-trained using science education data may improve model performance. However, the ideal type of data to contextualize pre-trained language model and improve the performance in automatically scoring student written responses remains unclear. Therefore, we employ different data in this study to contextualize both BERT and SciBERT models and compare their performance on automatic scoring of assessment tasks for scientific argumentation. We use three datasets to pre-train the model: 1) journal articles in science education, 2) a large dataset of students' written responses (sample size over 50,000), and 3) a small dataset of students' written responses of scientific argumentation tasks. Our experimental results show that in-domain training corpora constructed from science questions and responses improve language model performance on a wide variety of downstream tasks. Our study confirms the effectiveness of continual pre-training on domain-specific data in the education domain and demonstrates a generalizable strategy for automating science education tasks with high accuracy. We plan to release our data and SciEdBERT models for public use and community engagement.
IVJul 8, 2024
Potential of Multimodal Large Language Models for Data Mining of Medical Images and Free-text ReportsYutong Zhang, Yi Pan, Tianyang Zhong et al.
Medical images and radiology reports are crucial for diagnosing medical conditions, highlighting the importance of quantitative analysis for clinical decision-making. However, the diversity and cross-source heterogeneity of these data challenge the generalizability of current data-mining methods. Multimodal large language models (MLLMs) have recently transformed many domains, significantly affecting the medical field. Notably, Gemini-Vision-series (Gemini) and GPT-4-series (GPT-4) models have epitomized a paradigm shift in Artificial General Intelligence (AGI) for computer vision, showcasing their potential in the biomedical domain. In this study, we evaluated the performance of the Gemini, GPT-4, and 4 popular large models for an exhaustive evaluation across 14 medical imaging datasets, including 5 medical imaging categories (dermatology, radiology, dentistry, ophthalmology, and endoscopy), and 3 radiology report datasets. The investigated tasks encompass disease classification, lesion segmentation, anatomical localization, disease diagnosis, report generation, and lesion detection. Our experimental results demonstrated that Gemini-series models excelled in report generation and lesion detection but faces challenges in disease classification and anatomical localization. Conversely, GPT-series models exhibited proficiency in lesion segmentation and anatomical localization but encountered difficulties in disease diagnosis and lesion detection. Additionally, both the Gemini series and GPT series contain models that have demonstrated commendable generation efficiency. While both models hold promise in reducing physician workload, alleviating pressure on limited healthcare resources, and fostering collaboration between clinical practitioners and artificial intelligence technologies, substantial enhancements and comprehensive validations remain imperative before clinical deployment.
CLNov 5, 2023
Evaluating the Potential of Leading Large Language Models in Reasoning Biology QuestionsXinyu Gong, Jason Holmes, Yiwei Li et al.
Recent advances in Large Language Models (LLMs) have presented new opportunities for integrating Artificial General Intelligence (AGI) into biological research and education. This study evaluated the capabilities of leading LLMs, including GPT-4, GPT-3.5, PaLM2, Claude2, and SenseNova, in answering conceptual biology questions. The models were tested on a 108-question multiple-choice exam covering biology topics in molecular biology, biological techniques, metabolic engineering, and synthetic biology. Among the models, GPT-4 achieved the highest average score of 90 and demonstrated the greatest consistency across trials with different prompts. The results indicated GPT-4's proficiency in logical reasoning and its potential to aid biology research through capabilities like data analysis, hypothesis generation, and knowledge integration. However, further development and validation are still required before the promise of LLMs in accelerating biological discovery can be realized.
CLNov 7, 2023
Evaluating multiple large language models in pediatric ophthalmologyJason Holmes, Rui Peng, Yiwei Li et al.
IMPORTANCE The response effectiveness of different large language models (LLMs) and various individuals, including medical students, graduate students, and practicing physicians, in pediatric ophthalmology consultations, has not been clearly established yet. OBJECTIVE Design a 100-question exam based on pediatric ophthalmology to evaluate the performance of LLMs in highly specialized scenarios and compare them with the performance of medical students and physicians at different levels. DESIGN, SETTING, AND PARTICIPANTS This survey study assessed three LLMs, namely ChatGPT (GPT-3.5), GPT-4, and PaLM2, were assessed alongside three human cohorts: medical students, postgraduate students, and attending physicians, in their ability to answer questions related to pediatric ophthalmology. It was conducted by administering questionnaires in the form of test papers through the LLM network interface, with the valuable participation of volunteers. MAIN OUTCOMES AND MEASURES Mean scores of LLM and humans on 100 multiple-choice questions, as well as the answer stability, correlation, and response confidence of each LLM. RESULTS GPT-4 performed comparably to attending physicians, while ChatGPT (GPT-3.5) and PaLM2 outperformed medical students but slightly trailed behind postgraduate students. Furthermore, GPT-4 exhibited greater stability and confidence when responding to inquiries compared to ChatGPT (GPT-3.5) and PaLM2. CONCLUSIONS AND RELEVANCE Our results underscore the potential for LLMs to provide medical assistance in pediatric ophthalmology and suggest significant capacity to guide the education of medical students.
CLSep 12, 2024
LLM-POTUS Score: A Framework of Analyzing Presidential Debates with Large Language ModelsZhengliang Liu, Yiwei Li, Oleksandra Zolotarevych et al.
Large language models have demonstrated remarkable capabilities in natural language processing, yet their application to political discourse analysis remains underexplored. This paper introduces a novel approach to evaluating presidential debate performances using LLMs, addressing the longstanding challenge of objectively assessing debate outcomes. We propose a framework that analyzes candidates' "Policies, Persona, and Perspective" (3P) and how they resonate with the "Interests, Ideologies, and Identity" (3I) of four key audience groups: voters, businesses, donors, and politicians. Our method employs large language models to generate the LLM-POTUS Score, a quantitative measure of debate performance based on the alignment between 3P and 3I. We apply this framework to analyze transcripts from recent U.S. presidential debates, demonstrating its ability to provide nuanced, multi-dimensional assessments of candidate performances. Our results reveal insights into the effectiveness of different debating strategies and their impact on various audience segments. This study not only offers a new tool for political analysis but also explores the potential and limitations of using LLMs as impartial judges in complex social contexts. In addition, this framework provides individual citizens with an independent tool to evaluate presidential debate performances, which enhances democratic engagement and reduces reliance on potentially biased media interpretations and institutional influence, thereby strengthening the foundation of informed civic participation.
CLNov 7, 2023
Evaluating Large Language Models in OphthalmologyJason Holmes, Shuyuan Ye, Yiwei Li et al.
Purpose: The performance of three different large language models (LLMS) (GPT-3.5, GPT-4, and PaLM2) in answering ophthalmology professional questions was evaluated and compared with that of three different professional populations (medical undergraduates, medical masters, and attending physicians). Methods: A 100-item ophthalmology single-choice test was administered to three different LLMs (GPT-3.5, GPT-4, and PaLM2) and three different professional levels (medical undergraduates, medical masters, and attending physicians), respectively. The performance of LLM was comprehensively evaluated and compared with the human group in terms of average score, stability, and confidence. Results: Each LLM outperformed undergraduates in general, with GPT-3.5 and PaLM2 being slightly below the master's level, while GPT-4 showed a level comparable to that of attending physicians. In addition, GPT-4 showed significantly higher answer stability and confidence than GPT-3.5 and PaLM2. Conclusion: Our study shows that LLM represented by GPT-4 performs better in the field of ophthalmology. With further improvements, LLM will bring unexpected benefits in medical education and clinical decision making in the near future.
MED-PHOct 5, 2023
Benchmarking a foundation LLM on its ability to re-label structure names in accordance with the AAPM TG-263 reportJason Holmes, Lian Zhang, Yuzhen Ding et al.
Purpose: To introduce the concept of using large language models (LLMs) to re-label structure names in accordance with the American Association of Physicists in Medicine (AAPM) Task Group (TG)-263 standard, and to establish a benchmark for future studies to reference. Methods and Materials: The Generative Pre-trained Transformer (GPT)-4 application programming interface (API) was implemented as a Digital Imaging and Communications in Medicine (DICOM) storage server, which upon receiving a structure set DICOM file, prompts GPT-4 to re-label the structure names of both target volumes and normal tissues according to the AAPM TG-263. Three disease sites, prostate, head and neck, and thorax were selected for evaluation. For each disease site category, 150 patients were randomly selected for manually tuning the instructions prompt (in batches of 50) and 50 patients were randomly selected for evaluation. Structure names that were considered were those that were most likely to be relevant for studies utilizing structure contours for many patients. Results: The overall re-labeling accuracy of both target volumes and normal tissues for prostate, head and neck, and thorax cases was 96.0%, 98.5%, and 96.9% respectively. Re-labeling of target volumes was less accurate on average except for prostate - 100%, 93.1%, and 91.1% respectively. Conclusions: Given the accuracy of GPT-4 in re-labeling structure names of both target volumes and normal tissues as presented in this work, LLMs are poised to be the preferred method for standardizing structure names in radiation oncology, especially considering the rapid advancements in LLM capabilities that are likely to continue.
CVAug 23, 2024
Examining the Commitments and Difficulties Inherent in Multimodal Foundation Models for Street View ImageryZhenyuan Yang, Xuhui Lin, Qinyi He et al.
The emergence of Large Language Models (LLMs) and multimodal foundation models (FMs) has generated heightened interest in their applications that integrate vision and language. This paper investigates the capabilities of ChatGPT-4V and Gemini Pro for Street View Imagery, Built Environment, and Interior by evaluating their performance across various tasks. The assessments include street furniture identification, pedestrian and car counts, and road width measurement in Street View Imagery; building function classification, building age analysis, building height analysis, and building structure classification in the Built Environment; and interior room classification, interior design style analysis, interior furniture counts, and interior length measurement in Interior. The results reveal proficiency in length measurement, style analysis, question answering, and basic image understanding, but highlight limitations in detailed recognition and counting tasks. While zero-shot learning shows potential, performance varies depending on the problem domains and image complexities. This study provides new insights into the strengths and weaknesses of multimodal foundation models for practical challenges in Street View Imagery, Built Environment, and Interior. Overall, the findings demonstrate foundational multimodal intelligence, emphasizing the potential of FMs to drive forward interdisciplinary applications at the intersection of computer vision and language.
CLJan 10, 2024Code
TrustLLM: Trustworthiness in Large Language ModelsYue Huang, Lichao Sun, Haoran Wang et al.
Large language models (LLMs), exemplified by ChatGPT, have gained considerable attention for their excellent natural language processing capabilities. Nonetheless, these LLMs present many challenges, particularly in the realm of trustworthiness. Therefore, ensuring the trustworthiness of LLMs emerges as an important topic. This paper introduces TrustLLM, a comprehensive study of trustworthiness in LLMs, including principles for different dimensions of trustworthiness, established benchmark, evaluation, and analysis of trustworthiness for mainstream LLMs, and discussion of open challenges and future directions. Specifically, we first propose a set of principles for trustworthy LLMs that span eight different dimensions. Based on these principles, we further establish a benchmark across six dimensions including truthfulness, safety, fairness, robustness, privacy, and machine ethics. We then present a study evaluating 16 mainstream LLMs in TrustLLM, consisting of over 30 datasets. Our findings firstly show that in general trustworthiness and utility (i.e., functional effectiveness) are positively related. Secondly, our observations reveal that proprietary LLMs generally outperform most open-source counterparts in terms of trustworthiness, raising concerns about the potential risks of widely accessible open-source LLMs. However, a few open-source LLMs come very close to proprietary ones. Thirdly, it is important to note that some LLMs may be overly calibrated towards exhibiting trustworthiness, to the extent that they compromise their utility by mistakenly treating benign prompts as harmful and consequently not responding. Finally, we emphasize the importance of ensuring transparency not only in the models themselves but also in the technologies that underpin trustworthiness. Knowing the specific trustworthy technologies that have been employed is crucial for analyzing their effectiveness.