Qingqing Zhu

Shubo Tian, Qiao Jin, Lana Yeganova et al. · tsinghua

ChatGPT has drawn considerable attention from both the general public and domain experts with its remarkable text generation capabilities. This has subsequently led to the emergence of diverse applications in the field of biomedicine and health. In this work, we examine the diverse applications of large language models (LLMs), such as ChatGPT, in biomedicine and health. Specifically we explore the areas of biomedical information retrieval, question answering, medical text summarization, information extraction, and medical education, and investigate whether LLMs possess the transformative power to revolutionize these tasks or whether the distinct complexities of biomedical domain presents unique challenges. Following an extensive literature survey, we find that significant advances have been made in the field of text generation tasks, surpassing the previous state-of-the-art methods. For other applications, the advances have been modest. Overall, LLMs have not yet revolutionized biomedicine, but recent rapid progress indicates that such methods hold great potential to provide valuable means for accelerating discovery and improving health. We also find that the use of LLMs, like ChatGPT, in the fields of biomedicine and health entails various risks and challenges, including fabricated information in its generated responses, as well as legal and privacy concerns associated with sensitive patient data. We believe this survey can provide a comprehensive and timely overview to biomedical researchers and healthcare practitioners on the opportunities and challenges associated with using ChatGPT and other LLMs for transforming biomedicine and health.

Qingqing Zhu, Tejas Sudharshan Mathai, Pritam Mukherjee et al.

Despite the reduction in turn-around times in radiology reports with the use of speech recognition software, persistent communication errors can significantly impact the interpretation of the radiology report. Pre-filling a radiology report holds promise in mitigating reporting errors, and despite efforts in the literature to generate medical reports, there exists a lack of approaches that exploit the longitudinal nature of patient visit records in the MIMIC-CXR dataset. To address this gap, we propose to use longitudinal multi-modal data, i.e., previous patient visit CXR, current visit CXR, and previous visit report, to pre-fill the 'findings' section of a current patient visit report. We first gathered the longitudinal visit information for 26,625 patients from the MIMIC-CXR dataset and created a new dataset called Longitudinal-MIMIC. With this new dataset, a transformer-based model was trained to capture the information from longitudinal patient visit records containing multi-modal data (CXR images + reports) via a cross-attention-based multi-modal fusion module and a hierarchical memory-driven decoder. In contrast to previous work that only uses current visit data as input to train a model, our work exploits the longitudinal information available to pre-fill the 'findings' section of radiology reports. Experiments show that our approach outperforms several recent approaches. Code will be published at https://github.com/CelestialShine/Longitudinal-Chest-X-Ray.

Zhaoyi Sun, Mingquan Lin, Qingqing Zhu et al. · uw

Computer-assisted diagnostic and prognostic systems of the future should be capable of simultaneously processing multimodal data. Multimodal deep learning (MDL), which involves the integration of multiple sources of data, such as images and text, has the potential to revolutionize the analysis and interpretation of biomedical data. However, it only caught researchers' attention recently. To this end, there is a critical need to conduct a systematic review on this topic, identify the limitations of current work, and explore future directions. In this scoping review, we aim to provide a comprehensive overview of the current state of the field and identify key concepts, types of studies, and research gaps with a focus on biomedical images and texts joint learning, mainly because these two were the most commonly available data types in MDL research. This study reviewed the current uses of multimodal deep learning on five tasks: (1) Report generation, (2) Visual question answering, (3) Cross-modal retrieval, (4) Computer-aided diagnosis, and (5) Semantic segmentation. Our results highlight the diverse applications and potential of MDL and suggest directions for future research in the field. We hope our review will facilitate the collaboration of natural language processing (NLP) and medical imaging communities and support the next generation of decision-making and computer-assisted diagnostic system development.

Qingqing Zhu, Qiao Jin, Tejas S. Mathai et al.

Artificial intelligence (AI) can automatically delineate lesions on computed tomography (CT) and generate radiology report content, yet progress is limited by the scarcity of publicly available CT datasets with lesion-level annotations. To bridge this gap, we introduce CT-Bench, a first-of-its-kind benchmark dataset comprising two components: a Lesion Image and Metadata Set containing 20,335 lesions from 7,795 CT studies with bounding boxes, descriptions, and size information, and a multitask visual question answering benchmark with 2,850 QA pairs covering lesion localization, description, size estimation, and attribute categorization. Hard negative examples are included to reflect real-world diagnostic challenges. We evaluate multiple state-of-the-art multimodal models, including vision-language and medical CLIP variants, by comparing their performance to radiologist assessments, demonstrating the value of CT-Bench as a comprehensive benchmark for lesion analysis. Moreover, fine-tuning models on the Lesion Image and Metadata Set yields significant performance gains across both components, underscoring the clinical utility of CT-Bench.

Rezarta Islamaj, Robert Leaman, Joey Chan et al.

Evaluating large language models (LLMs) in the biomedical domain requires benchmarks that can distinguish reasoning from pattern matching and remain discriminative as model capabilities improve. Existing biomedical question answering (QA) benchmarks are limited in this respect. Multiple-choice formats can allow models to succeed through answer elimination rather than inference, while widely circulated exam-style datasets are increasingly vulnerable to performance saturation and training data contamination. Multi-hop reasoning, defined as the ability to integrate information across multiple sources to derive an answer, is central to clinically meaningful tasks such as diagnostic support, literature-based discovery, and hypothesis generation, yet remains underrepresented in current biomedical QA benchmarks. MedHopQA is a disease-centered multi-hop reasoning benchmark consisting of 1,000 expert-curated question-answer pairs introduced as a shared task at BioCreative IX. Each question requires synthesis of information across two distinct Wikipedia articles, and answers are provided in an open-ended free-text format. Gold annotations are augmented with ontology-grounded synonym sets from MONDO, NCBI Gene, and NCBI Taxonomy to support both lexical and concept-level evaluation. MedHopQA was constructed through a structured process combining human annotation, triage, iterative verification, and LLM-as-a-judge validation. To reduce leaderboard gaming and contamination risk, the 1,000 scored questions are embedded within a publicly downloadable set of 10,000 questions, with answers withheld, on a CodaBench leaderboard. MedHopQA provides both a benchmark and a reusable framework for constructing future biomedical QA datasets that prioritize compositional reasoning, saturation resistance, and contamination resistance as core design constraints.

Joey Chan, Yikun Han, Jingyuan Chen et al.

Plain Language Summaries (PLS) aim to make research accessible to lay readers, but they are typically written in a one-size-fits-all style that ignores differences in readers' information needs and comprehension. In health contexts, this limitation is particularly important because misunderstanding scientific information can affect real-world decisions. Large language models (LLMs) offer new opportunities for personalizing PLS, but it remains unclear whether personalization helps, which strategies are most effective, and how to balance personalization with safety. We introduce ReLay, a dataset of 300 participant--PLS pairs from 50 lay participants in both static (expert-written) and interactive (LLM-personalized) settings. ReLay includes user characteristics, health information needs, information-seeking behavior, comprehension outcomes, interaction logs, and quality ratings. We use ReLay to evaluate five LLMs across two personalization methods. Personalization improves comprehension and perceived quality, but it also raises the risk of reinforcing user biases and introducing hallucinations, revealing a trade-off between personalization and safety. These findings highlight the need for personalization methods that are both effective and trustworthy for diverse lay audiences.

Ruida Cheng, Tejas Sudharshan Mathai, Pritam Mukherjee et al.

Segmentation of lesions on CT enables automatic measurement for clinical assessment of chronic diseases (e.g., lymphoma). Integrating large language models (LLMs) into the lesion segmentation workflow offers the potential to combine imaging features with descriptions of lesion characteristics from the radiology reports. In this study, we investigate the feasibility of integrating text into the Swin-UMamba architecture for the task of lesion segmentation. The publicly available ULS23 DeepLesion dataset was used along with short-form descriptions of the findings from the reports. On the test dataset, a high Dice Score of 82% and low Hausdorff distance of 6.58 (pixels) was obtained for lesion segmentation. The proposed Text-Swin-UMamba model outperformed prior approaches: 37% improvement over the LLM-driven LanGuideMedSeg model (p < 0.001),and surpassed the purely image-based xLSTM-UNet and nnUNet models by 1.74% and 0.22%, respectively. The dataset and code can be accessed at https://github.com/ruida/LLM-Swin-UMamba

Xiuying Chen, Mingzhe Li, Shen Gao et al.

A proficient summarization model should exhibit both flexibility -- the capacity to handle a range of in-domain summarization tasks, and adaptability -- the competence to acquire new knowledge and adjust to unseen out-of-domain tasks. Unlike large language models (LLMs) that achieve this through parameter scaling, we propose a more parameter-efficient approach in this study. Our motivation rests on the principle that the general summarization ability to capture salient information can be shared across different tasks, while the domain-specific summarization abilities need to be distinct and tailored. Concretely, we propose MoeSumm, a Mixture-of-Expert Summarization architecture, which utilizes a main expert for gaining the general summarization capability and deputy experts that selectively collaborate to meet specific summarization task requirements. We further propose a max-margin loss to stimulate the separation of these abilities. Our model's distinct separation of general and domain-specific summarization abilities grants it with notable flexibility and adaptability, all while maintaining parameter efficiency. MoeSumm achieves flexibility by managing summarization across multiple domains with a single model, utilizing a shared main expert and selected deputy experts. It exhibits adaptability by tailoring deputy experts to cater to out-of-domain few-shot and zero-shot scenarios. Experimental results on 11 datasets show the superiority of our model compared with recent baselines and LLMs. We also provide statistical and visual evidence of the distinct separation of the two abilities in MoeSumm (https://github.com/iriscxy/MoE_Summ).

Benjamin Hou, Qingqing Zhu, Tejas Sudarshan Mathai et al.

In this paper, we introduce DRR-RATE, a large-scale synthetic chest X-ray dataset derived from the recently released CT-RATE dataset. DRR-RATE comprises of 50,188 frontal Digitally Reconstructed Radiographs (DRRs) from 21,304 unique patients. Each image is paired with a corresponding radiology text report and binary labels for 18 pathology classes. Given the controllable nature of DRR generation, it facilitates the inclusion of lateral view images and images from any desired viewing position. This opens up avenues for research into new and novel multimodal applications involving paired CT, X-ray images from various views, text, and binary labels. We demonstrate the applicability of DRR-RATE alongside existing large-scale chest X-ray resources, notably the CheXpert dataset and CheXnet model. Experiments demonstrate that CheXnet, when trained and tested on the DRR-RATE dataset, achieves sufficient to high AUC scores for the six common pathologies cited in common literature: Atelectasis, Cardiomegaly, Consolidation, Lung Lesion, Lung Opacity, and Pleural Effusion. Additionally, CheXnet trained on the CheXpert dataset can accurately identify several pathologies, even when operating out of distribution. This confirms that the generated DRR images effectively capture the essential pathology features from CT images. The dataset and labels are publicly accessible at https://huggingface.co/datasets/farrell236/DRR-RATE.

Qiao Jin, Zhizheng Wang, Yifan Yang et al.

Clinical calculators play a vital role in healthcare by offering accurate evidence-based predictions for various purposes such as prognosis. Nevertheless, their widespread utilization is frequently hindered by usability challenges, poor dissemination, and restricted functionality. Augmenting large language models with extensive collections of clinical calculators presents an opportunity to overcome these obstacles and improve workflow efficiency, but the scalability of the manual curation process poses a significant challenge. In response, we introduce AgentMD, a novel language agent capable of curating and applying clinical calculators across various clinical contexts. Using the published literature, AgentMD has automatically curated a collection of 2,164 diverse clinical calculators with executable functions and structured documentation, collectively named RiskCalcs. Manual evaluations show that RiskCalcs tools achieve an accuracy of over 80% on three quality metrics. At inference time, AgentMD can automatically select and apply the relevant RiskCalcs tools given any patient description. On the newly established RiskQA benchmark, AgentMD significantly outperforms chain-of-thought prompting with GPT-4 (87.7% vs. 40.9% in accuracy). Additionally, we also applied AgentMD to real-world clinical notes for analyzing both population-level and risk-level patient characteristics. In summary, our study illustrates the utility of language agents augmented with clinical calculators for healthcare analytics and patient care.

Qiao Jin, Nicholas Wan, Robert Leaman et al.

Large language models (LLMs) represent a transformative class of AI tools capable of revolutionizing various aspects of healthcare by generating human-like responses across diverse contexts and adapting to novel tasks following human instructions. Their potential application spans a broad range of medical tasks, such as clinical documentation, matching patients to clinical trials, and answering medical questions. In this primer paper, we propose an actionable guideline to help healthcare professionals more efficiently utilize LLMs in their work, along with a set of best practices. This approach consists of several main phases, including formulating the task, choosing LLMs, prompt engineering, fine-tuning, and deployment. We start with the discussion of critical considerations in identifying healthcare tasks that align with the core capabilities of LLMs and selecting models based on the selected task and data, performance requirements, and model interface. We then review the strategies, such as prompt engineering and fine-tuning, to adapt standard LLMs to specialized medical tasks. Deployment considerations, including regulatory compliance, ethical guidelines, and continuous monitoring for fairness and bias, are also discussed. By providing a structured step-by-step methodology, this tutorial aims to equip healthcare professionals with the tools necessary to effectively integrate LLMs into clinical practice, ensuring that these powerful technologies are applied in a safe, reliable, and impactful manner.

Qingqing Zhu, Xiuying Chen, Qiao Jin et al.

In radiology, Artificial Intelligence (AI) has significantly advanced report generation, but automatic evaluation of these AI-produced reports remains challenging. Current metrics, such as Conventional Natural Language Generation (NLG) and Clinical Efficacy (CE), often fall short in capturing the semantic intricacies of clinical contexts or overemphasize clinical details, undermining report clarity. To overcome these issues, our proposed method synergizes the expertise of professional radiologists with Large Language Models (LLMs), like GPT-3.5 and GPT-4 1. Utilizing In-Context Instruction Learning (ICIL) and Chain of Thought (CoT) reasoning, our approach aligns LLM evaluations with radiologist standards, enabling detailed comparisons between human and AI generated reports. This is further enhanced by a Regression model that aggregates sentence evaluation scores. Experimental results show that our "Detailed GPT-4 (5-shot)" model achieves a 0.48 score, outperforming the METEOR metric by 0.19, while our "Regressed GPT-4" model shows even greater alignment with expert evaluations, exceeding the best existing metric by a 0.35 margin. Moreover, the robustness of our explanations has been validated through a thorough iterative strategy. We plan to publicly release annotations from radiology experts, setting a new standard for accuracy in future assessments. This underscores the potential of our approach in enhancing the quality assessment of AI-driven medical reports.

Yifan Yang, Qiao Jin, Qingqing Zhu et al.

Large Language Models (LLMs) have gained significant attention in the medical domain for their human-level capabilities, leading to increased efforts to explore their potential in various healthcare applications. However, despite such a promising future, there are multiple challenges and obstacles that remain for their real-world uses in practical settings. This work discusses key challenges for LLMs in medical applications from four unique aspects: operational vulnerabilities, ethical and social considerations, performance and assessment difficulties, and legal and regulatory compliance. Addressing these challenges is crucial for leveraging LLMs to their full potential and ensuring their responsible integration into healthcare.

Xiuying Chen, Tairan Wang, Qingqing Zhu et al.

The summarization capabilities of pretrained and large language models (LLMs) have been widely validated in general areas, but their use in scientific corpus, which involves complex sentences and specialized knowledge, has been less assessed. This paper presents conceptual and experimental analyses of scientific summarization, highlighting the inadequacies of traditional evaluation methods, such as $n$-gram, embedding comparison, and QA, particularly in providing explanations, grasping scientific concepts, or identifying key content. Subsequently, we introduce the Facet-aware Metric (FM), employing LLMs for advanced semantic matching to evaluate summaries based on different aspects. This facet-aware approach offers a thorough evaluation of abstracts by decomposing the evaluation task into simpler subtasks.Recognizing the absence of an evaluation benchmark in this domain, we curate a Facet-based scientific summarization Dataset (FD) with facet-level annotations. Our findings confirm that FM offers a more logical approach to evaluating scientific summaries. In addition, fine-tuned smaller models can compete with LLMs in scientific contexts, while LLMs have limitations in learning from in-context information in scientific domains. This suggests an area for future enhancement of LLMs.

Qingqing Zhu, Benjamin Hou, Tejas S. Mathai et al.

Automatically interpreting CT scans can ease the workload of radiologists. However, this is challenging mainly due to the scarcity of adequate datasets and reference standards for evaluation. This study aims to bridge this gap by introducing a novel evaluation framework, named ``GPTRadScore''. This framework assesses the capabilities of multi-modal LLMs, such as GPT-4 with Vision (GPT-4V), Gemini Pro Vision, LLaVA-Med, and RadFM, in generating descriptions for prospectively-identified findings. By employing a decomposition technique based on GPT-4, GPTRadScore compares these generated descriptions with gold-standard report sentences, analyzing their accuracy in terms of body part, location, and type of finding. Evaluations demonstrated a high correlation with clinician assessments and highlighted its potential over traditional metrics, such as BLEU, METEOR, and ROUGE. Furthermore, to contribute to future studies, we plan to release a benchmark dataset annotated by clinicians. Using GPTRadScore, we found that while GPT-4V and Gemini Pro Vision fare better, their performance revealed significant areas for improvement, primarily due to limitations in the dataset used for training these models. To demonstrate this potential, RadFM was fine-tuned and it resulted in significant accuracy improvements: location accuracy rose from 3.41\% to 12.8\%, body part accuracy from 29.12\% to 53\%, and type accuracy from 9.24\% to 30\%, thereby validating our hypothesis.

Zhizheng Wang, Chi-Ping Day, Chih-Hsuan Wei et al.

Gene set analysis (GSA) is a foundational approach for interpreting genomic data of diseases by linking genes to biological processes. However, conventional GSA methods overlook clinical context of the analyses, often generating long lists of enriched pathways with redundant, nonspecific, or irrelevant results. Interpreting these requires extensive, ad-hoc manual effort, reducing both reliability and reproducibility. To address this limitation, we introduce cGSA, a novel AI-driven framework that enhances GSA by incorporating context-aware pathway prioritization. cGSA integrates gene cluster detection, enrichment analysis, and large language models to identify pathways that are not only statistically significant but also biologically meaningful. Benchmarking on 102 manually curated gene sets across 19 diseases and ten disease-related biological mechanisms shows that cGSA outperforms baseline methods by over 30%, with expert validation confirming its increased precision and interpretability. Two independent case studies in melanoma and breast cancer further demonstrate its potential to uncover context-specific insights and support targeted hypothesis generation.

Xiuying Chen, Shen Gao, Mingzhe Li et al.

Nowadays, neural text generation has made tremendous progress in abstractive summarization tasks. However, most of the existing summarization models take in the whole document all at once, which sometimes cannot meet the needs in practice. Practically, social text streams such as news events and tweets keep growing from time to time, and can only be fed to the summarization system step by step. Hence, in this paper, we propose the task of Stepwise Summarization, which aims to generate a new appended summary each time a new document is proposed. The appended summary should not only summarize the newly added content but also be coherent with the previous summary, to form an up-to-date complete summary. To tackle this challenge, we design an adversarial learning model, named Stepwise Summary Generator (SSG). First, SSG selectively processes the new document under the guidance of the previous summary, obtaining polished document representation. Next, SSG generates the summary considering both the previous summary and the document. Finally, a convolutional-based discriminator is employed to determine whether the newly generated summary is coherent with the previous summary. For the experiment, we extend the traditional two-step update summarization setting to a multi-step stepwise setting, and re-propose a large-scale stepwise summarization dataset based on a public story generation dataset. Extensive experiments on this dataset show that SSG achieves state-of-the-art performance in terms of both automatic metrics and human evaluations. Ablation studies demonstrate the effectiveness of each module in our framework. We also discuss the benefits and limitations of recent large language models on this task.

Zekun Wang, Ge Zhang, Kexin Yang et al.

Interactive Natural Language Processing (iNLP) has emerged as a novel paradigm within the field of NLP, aimed at addressing limitations in existing frameworks while aligning with the ultimate goals of artificial intelligence. This paradigm considers language models as agents capable of observing, acting, and receiving feedback iteratively from external entities. Specifically, language models in this context can: (1) interact with humans for better understanding and addressing user needs, personalizing responses, aligning with human values, and improving the overall user experience; (2) interact with knowledge bases for enriching language representations with factual knowledge, enhancing the contextual relevance of responses, and dynamically leveraging external information to generate more accurate and informed responses; (3) interact with models and tools for effectively decomposing and addressing complex tasks, leveraging specialized expertise for specific subtasks, and fostering the simulation of social behaviors; and (4) interact with environments for learning grounded representations of language, and effectively tackling embodied tasks such as reasoning, planning, and decision-making in response to environmental observations. This paper offers a comprehensive survey of iNLP, starting by proposing a unified definition and framework of the concept. We then provide a systematic classification of iNLP, dissecting its various components, including interactive objects, interaction interfaces, and interaction methods. We proceed to delve into the evaluation methodologies used in the field, explore its diverse applications, scrutinize its ethical and safety issues, and discuss prospective research directions. This survey serves as an entry point for researchers who are interested in this rapidly evolving area and offers a broad view of the current landscape and future trajectory of iNLP.