arXiv subjects

Dajiang Zhu

Publications and source records attributed to Dajiang Zhu.

At least 55 records · Page 3Linked to original sources

arXiv2024

Role of Data-driven Regional Growth Model in Shaping Brain Folding Patterns

The surface morphology of the developing mammalian brain is crucial for understanding brain function and dysfunction. Computational modeling offers valuable insights into the underlying mechanisms for early brain folding. Recent findings indicate significant regional variations in brain tissue growth, while the role of these variations in cortical development remains unclear. In this study, we unprecedently explored how regional cortical growth affects brain folding patterns using computational simulation. We first developed growth models for typical cortical regions using machine learning (ML)-assisted symbolic regression, based on longitudinal real surface expansion and cortical thickness data from prenatal and infant brains derived from over 1,000 MRI scans of 735 pediatric subjects with ages ranging from 29 post-menstrual weeks to 24 months. These models were subsequently integrated into computational software to simulate cortical development with anatomically realistic geometric models. We comprehensively quantified the resulting folding patterns using multiple metrics such as mean curvature, sulcal depth, and gyrification index. Our results demonstrate that regional growth models generate complex brain folding patterns that more closely match actual brains structures, both quantitatively and qualitatively, compared to conventional uniform growth models. Growth magnitude plays a dominant role in shaping folding patterns, while growth trajectory has a minor influence. Moreover, multi-region models better capture the intricacies of brain folding than single-region models. Our results underscore the necessity and importance of incorporating regional growth heterogeneity into brain folding simulations, which could enhance early diagnosis and treatment of cortical malformations and neurodevelopmental disorders such as cerebral palsy and autism.

q-bio.NC↗

arXiv2024

Brain Dialogue Interface (BDI): A User-Friendly fMRI Model for Interactive Brain Decoding

Brain decoding techniques are essential for understanding the neurocognitive system. Although numerous methods have been introduced in this field, accurately aligning complex external stimuli with brain activities remains a formidable challenge. To alleviate alignment difficulties, many studies have simplified their models by employing single-task paradigms and establishing direct links between brain/world through classification strategies. Despite improvements in decoding accuracy, this strategy frequently encounters issues with generality when adapting these models to various task paradigms. To address this issue, this study introduces a user-friendly decoding model that enables dynamic communication with the brain, as opposed to the static decoding approaches utilized by traditional studies. The model functions as a brain simulator, allowing for interactive engagement with the brain and enabling the decoding of a subject's experiences through dialogue-like queries. Uniquely, our model is trained in a completely unsupervised and task-free manner. Our experiments demonstrate the feasibility and versatility of our proposed method. Notably, our model demonstrates exceptional capabilities in signal compression, successfully representing the entire brain signal of approximately 185,751 voxels with just 32 signals. Furthermore, we show how our model can integrate seamlessly with multimodal models, thus enhancing the potential for controlling brain decoding through textual or image inputs.

q-bio.NC↗

arXiv2024

Eye-gaze Guided Multi-modal Alignment for Medical Representation Learning

In the medical multi-modal frameworks, the alignment of cross-modality features presents a significant challenge. However, existing works have learned features that are implicitly aligned from the data, without considering the explicit relationships in the medical context. This data-reliance may lead to low generalization of the learned alignment relationships. In this work, we propose the Eye-gaze Guided Multi-modal Alignment (EGMA) framework to harness eye-gaze data for better alignment of medical visual and textual features. We explore the natural auxiliary role of radiologists' eye-gaze data in aligning medical images and text, and introduce a novel approach by using eye-gaze data, collected synchronously by radiologists during diagnostic evaluations. We conduct downstream tasks of image classification and image-text retrieval on four medical datasets, where EGMA achieved state-of-the-art performance and stronger generalization across different datasets. Additionally, we explore the impact of varying amounts of eye-gaze data on model performance, highlighting the feasibility and utility of integrating this auxiliary data into multi-modal alignment framework.

cs.CV↗

arXiv2024

An Iterative Optimizing Framework for Radiology Report Summarization with ChatGPT

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.

cs.CL↗

arXiv2024

Prompt Engineering for Healthcare: Methodologies and Applications

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.

cs.AI↗

arXiv2024

Radiology-GPT: A Large Language Model for Radiology

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.

cs.CL↗

arXiv2024

SAMAug: Point Prompt Augmentation for Segment Anything Model

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

cs.CV↗

arXiv2024

InterLUDE: Interactions between Labeled and Unlabeled Data to Enhance Semi-Supervised Learning

Semi-supervised learning (SSL) seeks to enhance task performance by training on both labeled and unlabeled data. Mainstream SSL image classification methods mostly optimize a loss that additively combines a supervised classification objective with a regularization term derived solely from unlabeled data. This formulation neglects the potential for interaction between labeled and unlabeled images. In this paper, we introduce InterLUDE, a new approach to enhance SSL made of two parts that each benefit from labeled-unlabeled interaction. The first part, embedding fusion, interpolates between labeled and unlabeled embeddings to improve representation learning. The second part is a new loss, grounded in the principle of consistency regularization, that aims to minimize discrepancies in the model's predictions between labeled versus unlabeled inputs. Experiments on standard closed-set SSL benchmarks and a medical SSL task with an uncurated unlabeled set show clear benefits to our approach. On the STL-10 dataset with only 40 labels, InterLUDE achieves 3.2% error rate, while the best previous method reports 14.9%.

cs.CV↗

arXiv2023

Holistic Evaluation of GPT-4V for Biomedical Imaging

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.

eess.IV↗

arXiv2023

RadOnc-GPT: A Large Language Model for Radiation Oncology

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.

physics.med-ph↗

arXiv2023

ChatRadio-Valuer: A Chat Large Language Model for Generalizable Radiology Report Generation Based on Multi-institution and Multi-system Data

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.

cs.CL↗

arXiv2023

PolicyGPT: Automated Analysis of Privacy Policies with Large Language Models

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.

cs.CL↗

arXiv2023

Artificial General Intelligence for Radiation Oncology

The emergence of artificial general intelligence (AGI) is transforming radiation oncology. As prominent vanguards of AGI, large language models (LLMs) such as GPT-4 and PaLM 2 can process extensive texts and large vision models (LVMs) such as the Segment Anything Model (SAM) can process extensive imaging data to enhance the efficiency and precision of radiation therapy. This paper explores full-spectrum applications of AGI across radiation oncology including initial consultation, simulation, treatment planning, treatment delivery, treatment verification, and patient follow-up. The fusion of vision data with LLMs also creates powerful multimodal models that elucidate nuanced clinical patterns. Together, AGI promises to catalyze a shift towards data-driven, personalized radiation therapy. However, these models should complement human expertise and care. This paper provides an overview of how AGI can transform radiation oncology to elevate the standard of patient care in radiation oncology, with the key insight being AGI's ability to exploit multimodal clinical data at scale.

physics.med-ph↗

arXiv2023

Radiology-Llama2: Best-in-Class Large Language Model for Radiology

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.

cs.CL↗

arXiv2023

Summary of ChatGPT-Related Research and Perspective Towards the Future of Large Language Models

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.

cs.CL↗

arXiv2023

Hierarchical Semantic Tree Concept Whitening for Interpretable Image Classification

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.

cs.CV↗

arXiv2023

Exploring Multimodal Approaches for Alzheimer's Disease Detection Using Patient Speech Transcript and Audio Data

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.

eess.AS↗

arXiv2023

Segment Anything Model (SAM) for Radiation Oncology

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.

eess.IV↗