arXiv subjects

Tianbin Li

Publications and source records attributed to Tianbin Li.

At least 37 records · Page 2Linked to original sources

arXiv2025

S2-UniSeg: Fast Universal Agglomerative Pooling for Scalable Segment Anything without Supervision

Recent self-supervised image segmentation models have achieved promising performance on semantic segmentation and class-agnostic instance segmentation. However, their pretraining schedule is multi-stage, requiring a time-consuming pseudo-masks generation process between each training epoch. This time-consuming offline process not only makes it difficult to scale with training dataset size, but also leads to sub-optimal solutions due to its discontinuous optimization routine. To solve these, we first present a novel pseudo-mask algorithm, Fast Universal Agglomerative Pooling (UniAP). Each layer of UniAP can identify groups of similar nodes in parallel, allowing to generate both semantic-level and instance-level and multi-granular pseudo-masks within ens of milliseconds for one image. Based on the fast UniAP, we propose the Scalable Self-Supervised Universal Segmentation (S2-UniSeg), which employs a student and a momentum teacher for continuous pretraining. A novel segmentation-oriented pretext task, Query-wise Self-Distillation (QuerySD), is proposed to pretrain S2-UniSeg to learn the local-to-global correspondences. Under the same setting, S2-UniSeg outperforms the SOTA UnSAM model, achieving notable improvements of AP+6.9 on COCO, AR+11.1 on UVO, PixelAcc+4.5 on COCOStuff-27, RQ+8.0 on Cityscapes. After scaling up to a larger 2M-image subset of SA-1B, S2-UniSeg further achieves performance gains on all four benchmarks. Our code and pretrained models are available at https://github.com/bio-mlhui/S2-UniSeg

cs.CV↗

arXiv2025

RetinaLogos: Fine-Grained Synthesis of High-Resolution Retinal Images Through Captions

The scarcity of high-quality, labelled retinal imaging data, which presents a significant challenge in the development of machine learning models for ophthalmology, hinders progress in the field. Existing methods for synthesising Colour Fundus Photographs (CFPs) largely rely on predefined disease labels, which restricts their ability to generate images that reflect fine-grained anatomical variations, subtle disease stages, and diverse pathological features beyond coarse class categories. To overcome these challenges, we first introduce an innovative pipeline that creates a large-scale, captioned retinal dataset comprising 1.4 million entries, called RetinaLogos-1400k. Specifically, RetinaLogos-1400k uses the visual language model(VLM) to describe retinal conditions and key structures, such as optic disc configuration, vascular distribution, nerve fibre layers, and pathological features. Building on this dataset, we employ a novel three-step training framework, RetinaLogos, which enables fine-grained semantic control over retinal images and accurately captures different stages of disease progression, subtle anatomical variations, and specific lesion types. Through extensive experiments, our method demonstrates superior performance across multiple datasets, with 62.07% of text-driven synthetic CFPs indistinguishable from real ones by ophthalmologists. Moreover, the synthetic data improves accuracy by 5%-10% in diabetic retinopathy grading and glaucoma detection. Codes are available at https://github.com/uni-medical/retina-text2cfp.

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arXiv2025

Building a Human-Verified Clinical Reasoning Dataset via a Human LLM Hybrid Pipeline for Trustworthy Medical AI

Despite strong performance in medical question-answering, the clinical adoption of Large Language Models (LLMs) is critically hampered by their opaque 'black-box' reasoning, limiting clinician trust. This challenge is compounded by the predominant reliance of current medical LLMs on corpora from scientific literature or synthetic data, which often lack the granular expert validation and high clinical relevance essential for advancing their specialized medical capabilities. To address these critical gaps, we introduce a highly clinically relevant dataset with 31,247 medical question-answer pairs, each accompanied by expert-validated chain-of-thought (CoT) explanations. This resource, spanning multiple clinical domains, was curated via a scalable human-LLM hybrid pipeline: LLM-generated rationales were iteratively reviewed, scored, and refined by medical experts against a structured rubric, with substandard outputs revised through human effort or guided LLM regeneration until expert consensus. This publicly available dataset provides a vital source for the development of medical LLMs that capable of transparent and verifiable reasoning, thereby advancing safer and more interpretable AI in medicine.

cs.CV↗

arXiv2025

GMAI-VL-R1: Harnessing Reinforcement Learning for Multimodal Medical Reasoning

Recent advances in general medical AI have made significant strides, but existing models often lack the reasoning capabilities needed for complex medical decision-making. This paper presents GMAI-VL-R1, a multimodal medical reasoning model enhanced by reinforcement learning (RL) to improve its reasoning abilities. Through iterative training, GMAI-VL-R1 optimizes decision-making, significantly boosting diagnostic accuracy and clinical support. We also develop a reasoning data synthesis method, generating step-by-step reasoning data via rejection sampling, which further enhances the model's generalization. Experimental results show that after RL training, GMAI-VL-R1 excels in tasks such as medical image diagnosis and visual question answering. While the model demonstrates basic memorization with supervised fine-tuning, RL is crucial for true generalization. Our work establishes new evaluation benchmarks and paves the way for future advancements in medical reasoning models. Code, data, and model will be released at \href{https://github.com/uni-medical/GMAI-VL-R1}{this link}.

cs.CV↗

arXiv2025

GMAI-VL & GMAI-VL-5.5M: A Large Vision-Language Model and A Comprehensive Multimodal Dataset Towards General Medical AI

Despite significant advancements in general AI, its effectiveness in the medical domain is limited by the lack of specialized medical knowledge. To address this, we formulate GMAI-VL-5.5M, a multimodal medical dataset created by converting hundreds of specialized medical datasets with various annotations into high-quality image-text pairs. This dataset offers comprehensive task coverage, diverse modalities, and rich image-text data. Building upon this dataset, we develop GMAI-VL, a general medical vision-language model, with a three-stage training strategy that enhances the integration of visual and textual information. This approach significantly improves the model's ability to process multimodal data, supporting accurate diagnoses and clinical decision-making. Experiments show that GMAI-VL achieves state-of-the-art performance across various multimodal medical tasks, including visual question answering and medical image diagnosis.

cs.CV↗

arXiv2025

SlideChat: A Large Vision-Language Assistant for Whole-Slide Pathology Image Understanding

Despite the progress made by multimodal large language models (MLLMs) in computational pathology, they remain limited by a predominant focus on patch-level analysis, missing essential contextual information at the whole-slide level. The lack of large-scale instruction datasets and the gigapixel scale of whole slide images (WSIs) pose significant developmental challenges. In this paper, we present SlideChat, the first vision-language assistant capable of understanding gigapixel whole-slide images, exhibiting excellent multimodal conversational capability and response complex instruction across diverse pathology scenarios. To support its development, we created SlideInstruction, the largest instruction-following dataset for WSIs consisting of 4.2K WSI captions and 176K VQA pairs with multiple categories. Furthermore, we propose SlideBench, a multimodal benchmark that incorporates captioning and VQA tasks to assess SlideChat's capabilities in varied clinical settings such as microscopy, diagnosis. Compared to both general and specialized MLLMs, SlideChat exhibits exceptional capabilities achieving state-of-the-art performance on 18 of 22 tasks. For example, it achieved an overall accuracy of 81.17% on SlideBench-VQA (TCGA), and 54.15% on SlideBench-VQA (BCNB). Our code, data, and model is publicly accessible at https://uni-medical.github.io/SlideChat.github.io.

cs.CV↗

arXiv2024

OphCLIP: Hierarchical Retrieval-Augmented Learning for Ophthalmic Surgical Video-Language Pretraining

Surgical practice involves complex visual interpretation, procedural skills, and advanced medical knowledge, making surgical vision-language pretraining (VLP) particularly challenging due to this complexity and the limited availability of annotated data. To address the gap, we propose OphCLIP, a hierarchical retrieval-augmented vision-language pretraining framework specifically designed for ophthalmic surgical workflow understanding. OphCLIP leverages the OphVL dataset we constructed, a large-scale and comprehensive collection of over 375K hierarchically structured video-text pairs with tens of thousands of different combinations of attributes (surgeries, phases/operations/actions, instruments, medications, as well as more advanced aspects like the causes of eye diseases, surgical objectives, and postoperative recovery recommendations, etc). These hierarchical video-text correspondences enable OphCLIP to learn both fine-grained and long-term visual representations by aligning short video clips with detailed narrative descriptions and full videos with structured titles, capturing intricate surgical details and high-level procedural insights, respectively. Our OphCLIP also designs a retrieval-augmented pretraining framework to leverage the underexplored large-scale silent surgical procedure videos, automatically retrieving semantically relevant content to enhance the representation learning of narrative videos. Evaluation across 11 datasets for phase recognition and multi-instrument identification shows OphCLIP's robust generalization and superior performance.

cs.CV↗

arXiv2024

Interactive Medical Image Segmentation: A Benchmark Dataset and Baseline

Interactive Medical Image Segmentation (IMIS) has long been constrained by the limited availability of large-scale, diverse, and densely annotated datasets, which hinders model generalization and consistent evaluation across different models. In this paper, we introduce the IMed-361M benchmark dataset, a significant advancement in general IMIS research. First, we collect and standardize over 6.4 million medical images and their corresponding ground truth masks from multiple data sources. Then, leveraging the strong object recognition capabilities of a vision foundational model, we automatically generated dense interactive masks for each image and ensured their quality through rigorous quality control and granularity management. Unlike previous datasets, which are limited by specific modalities or sparse annotations, IMed-361M spans 14 modalities and 204 segmentation targets, totaling 361 million masks-an average of 56 masks per image. Finally, we developed an IMIS baseline network on this dataset that supports high-quality mask generation through interactive inputs, including clicks, bounding boxes, text prompts, and their combinations. We evaluate its performance on medical image segmentation tasks from multiple perspectives, demonstrating superior accuracy and scalability compared to existing interactive segmentation models. To facilitate research on foundational models in medical computer vision, we release the IMed-361M and model at https://github.com/uni-medical/IMIS-Bench.

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arXiv2024

GMAI-MMBench: A Comprehensive Multimodal Evaluation Benchmark Towards General Medical AI

Large Vision-Language Models (LVLMs) are capable of handling diverse data types such as imaging, text, and physiological signals, and can be applied in various fields. In the medical field, LVLMs have a high potential to offer substantial assistance for diagnosis and treatment. Before that, it is crucial to develop benchmarks to evaluate LVLMs' effectiveness in various medical applications. Current benchmarks are often built upon specific academic literature, mainly focusing on a single domain, and lacking varying perceptual granularities. Thus, they face specific challenges, including limited clinical relevance, incomplete evaluations, and insufficient guidance for interactive LVLMs. To address these limitations, we developed the GMAI-MMBench, the most comprehensive general medical AI benchmark with well-categorized data structure and multi-perceptual granularity to date. It is constructed from 284 datasets across 38 medical image modalities, 18 clinical-related tasks, 18 departments, and 4 perceptual granularities in a Visual Question Answering (VQA) format. Additionally, we implemented a lexical tree structure that allows users to customize evaluation tasks, accommodating various assessment needs and substantially supporting medical AI research and applications. We evaluated 50 LVLMs, and the results show that even the advanced GPT-4o only achieves an accuracy of 53.96%, indicating significant room for improvement. Moreover, we identified five key insufficiencies in current cutting-edge LVLMs that need to be addressed to advance the development of better medical applications. We believe that GMAI-MMBench will stimulate the community to build the next generation of LVLMs toward GMAI.

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arXiv2024

SAM-Med3D: Towards General-purpose Segmentation Models for Volumetric Medical Images

Existing volumetric medical image segmentation models are typically task-specific, excelling at specific target but struggling to generalize across anatomical structures or modalities. This limitation restricts their broader clinical use. In this paper, we introduce SAM-Med3D for general-purpose segmentation on volumetric medical images. Given only a few 3D prompt points, SAM-Med3D can accurately segment diverse anatomical structures and lesions across various modalities. To achieve this, we gather and process a large-scale 3D medical image dataset, SA-Med3D-140K, from a blend of public sources and licensed private datasets. This dataset includes 22K 3D images and 143K corresponding 3D masks. Then SAM-Med3D, a promptable segmentation model characterized by the fully learnable 3D structure, is trained on this dataset using a two-stage procedure and exhibits impressive performance on both seen and unseen segmentation targets. We comprehensively evaluate SAM-Med3D on 16 datasets covering diverse medical scenarios, including different anatomical structures, modalities, targets, and zero-shot transferability to new/unseen tasks. The evaluation shows the efficiency and efficacy of SAM-Med3D, as well as its promising application to diverse downstream tasks as a pre-trained model. Our approach demonstrates that substantial medical resources can be utilized to develop a general-purpose medical AI for various potential applications. Our dataset, code, and models are available at https://github.com/uni-medical/SAM-Med3D.

cs.CV↗

arXiv2024

PitVis-2023 Challenge: Workflow Recognition in videos of Endoscopic Pituitary Surgery

The field of computer vision applied to videos of minimally invasive surgery is ever-growing. Workflow recognition pertains to the automated recognition of various aspects of a surgery: including which surgical steps are performed; and which surgical instruments are used. This information can later be used to assist clinicians when learning the surgery; during live surgery; and when writing operation notes. The Pituitary Vision (PitVis) 2023 Challenge tasks the community to step and instrument recognition in videos of endoscopic pituitary surgery. This is a unique task when compared to other minimally invasive surgeries due to the smaller working space, which limits and distorts vision; and higher frequency of instrument and step switching, which requires more precise model predictions. Participants were provided with 25-videos, with results presented at the MICCAI-2023 conference as part of the Endoscopic Vision 2023 Challenge in Vancouver, Canada, on 08-Oct-2023. There were 18-submissions from 9-teams across 6-countries, using a variety of deep learning models. A commonality between the top performing models was incorporating spatio-temporal and multi-task methods, with greater than 50% and 10% macro-F1-score improvement over purely spacial single-task models in step and instrument recognition respectively. The PitVis-2023 Challenge therefore demonstrates state-of-the-art computer vision models in minimally invasive surgery are transferable to a new dataset, with surgery specific techniques used to enhance performance, progressing the field further. Benchmark results are provided in the paper, and the dataset is publicly available at: https://doi.org/10.5522/04/26531686.

cs.CV↗

arXiv2024

A Survey for Large Language Models in Biomedicine

Recent breakthroughs in large language models (LLMs) offer unprecedented natural language understanding and generation capabilities. However, existing surveys on LLMs in biomedicine often focus on specific applications or model architectures, lacking a comprehensive analysis that integrates the latest advancements across various biomedical domains. This review, based on an analysis of 484 publications sourced from databases including PubMed, Web of Science, and arXiv, provides an in-depth examination of the current landscape, applications, challenges, and prospects of LLMs in biomedicine, distinguishing itself by focusing on the practical implications of these models in real-world biomedical contexts. Firstly, we explore the capabilities of LLMs in zero-shot learning across a broad spectrum of biomedical tasks, including diagnostic assistance, drug discovery, and personalized medicine, among others, with insights drawn from 137 key studies. Then, we discuss adaptation strategies of LLMs, including fine-tuning methods for both uni-modal and multi-modal LLMs to enhance their performance in specialized biomedical contexts where zero-shot fails to achieve, such as medical question answering and efficient processing of biomedical literature. Finally, we discuss the challenges that LLMs face in the biomedicine domain including data privacy concerns, limited model interpretability, issues with dataset quality, and ethics due to the sensitive nature of biomedical data, the need for highly reliable model outputs, and the ethical implications of deploying AI in healthcare. To address these challenges, we also identify future research directions of LLM in biomedicine including federated learning methods to preserve data privacy and integrating explainable AI methodologies to enhance the transparency of LLMs.

cs.CL↗

arXiv2024

TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering

The structural similarities between protein sequences and natural languages have led to parallel advancements in deep learning across both domains. While large language models (LLMs) have achieved much progress in the domain of natural language processing, their potential in protein engineering remains largely unexplored. Previous approaches have equipped LLMs with protein understanding capabilities by incorporating external protein encoders, but this fails to fully leverage the inherent similarities between protein sequences and natural languages, resulting in sub-optimal performance and increased model complexity. To address this gap, we present TourSynbio-7B, the first multi-modal large model specifically designed for protein engineering tasks without external protein encoders. TourSynbio-7B demonstrates that LLMs can inherently learn to understand proteins as language. The model is post-trained and instruction fine-tuned on InternLM2-7B using ProteinLMDataset, a dataset comprising 17.46 billion tokens of text and protein sequence for self-supervised pretraining and 893K instructions for supervised fine-tuning. TourSynbio-7B outperforms GPT-4 on the ProteinLMBench, a benchmark of 944 manually verified multiple-choice questions, with 62.18% accuracy. Leveraging TourSynbio-7B's enhanced protein sequence understanding capability, we introduce TourSynbio-Agent, an innovative framework capable of performing various protein engineering tasks, including mutation analysis, inverse folding, protein folding, and visualization. TourSynbio-Agent integrates previously disconnected deep learning models in the protein engineering domain, offering a unified conversational user interface for improved usability. Finally, we demonstrate the efficacy of TourSynbio-7B and TourSynbio-Agent through two wet lab case studies on vanilla key enzyme modification and steroid compound catalysis.

q-bio.BM↗

arXiv2024

A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in comprehending protein sequences remains an open question, largely due to the absence of datasets linking protein sequences to descriptive text. Researchers have then attempted to adapt LLMs for protein understanding by integrating a protein sequence encoder with a pre-trained LLM. However, this adaptation raises a fundamental question: "Can LLMs, originally designed for NLP, effectively comprehend protein sequences as a form of language?" Current datasets fall short in addressing this question due to the lack of a direct correlation between protein sequences and corresponding text descriptions, limiting the ability to train and evaluate LLMs for protein understanding effectively. To bridge this gap, we introduce ProteinLMDataset, a dataset specifically designed for further self-supervised pretraining and supervised fine-tuning (SFT) of LLMs to enhance their capability for protein sequence comprehension. Specifically, ProteinLMDataset includes 17.46 billion tokens for pretraining and 893,000 instructions for SFT. Additionally, we present ProteinLMBench, the first benchmark dataset consisting of 944 manually verified multiple-choice questions for assessing the protein understanding capabilities of LLMs. ProteinLMBench incorporates protein-related details and sequences in multiple languages, establishing a new standard for evaluating LLMs' abilities in protein comprehension. The large language model InternLM2-7B, pretrained and fine-tuned on the ProteinLMDataset, outperforms GPT-4 on ProteinLMBench, achieving the highest accuracy score.

q-bio.QM↗

arXiv2024

SAM-Med3D-MoE: Towards a Non-Forgetting Segment Anything Model via Mixture of Experts for 3D Medical Image Segmentation

Volumetric medical image segmentation is pivotal in enhancing disease diagnosis, treatment planning, and advancing medical research. While existing volumetric foundation models for medical image segmentation, such as SAM-Med3D and SegVol, have shown remarkable performance on general organs and tumors, their ability to segment certain categories in clinical downstream tasks remains limited. Supervised Finetuning (SFT) serves as an effective way to adapt such foundation models for task-specific downstream tasks but at the cost of degrading the general knowledge previously stored in the original foundation model.To address this, we propose SAM-Med3D-MoE, a novel framework that seamlessly integrates task-specific finetuned models with the foundational model, creating a unified model at minimal additional training expense for an extra gating network. This gating network, in conjunction with a selection strategy, allows the unified model to achieve comparable performance of the original models in their respective tasks both general and specialized without updating any parameters of them.Our comprehensive experiments demonstrate the efficacy of SAM-Med3D-MoE, with an average Dice performance increase from 53 to 56.4 on 15 specific classes. It especially gets remarkable gains of 29.6, 8.5, 11.2 on the spinal cord, esophagus, and right hip, respectively. Additionally, it achieves 48.9 Dice on the challenging SPPIN2023 Challenge, significantly surpassing the general expert's performance of 32.3. We anticipate that SAM-Med3D-MoE can serve as a new framework for adapting the foundation model to specific areas in medical image analysis. Codes and datasets will be publicly available.

cs.CV↗

arXiv2024

OmniMedVQA: A New Large-Scale Comprehensive Evaluation Benchmark for Medical LVLM

Large Vision-Language Models (LVLMs) have demonstrated remarkable capabilities in various multimodal tasks. However, their potential in the medical domain remains largely unexplored. A significant challenge arises from the scarcity of diverse medical images spanning various modalities and anatomical regions, which is essential in real-world medical applications. To solve this problem, in this paper, we introduce OmniMedVQA, a novel comprehensive medical Visual Question Answering (VQA) benchmark. This benchmark is collected from 73 different medical datasets, including 12 different modalities and covering more than 20 distinct anatomical regions. Importantly, all images in this benchmark are sourced from authentic medical scenarios, ensuring alignment with the requirements of the medical field and suitability for evaluating LVLMs. Through our extensive experiments, we have found that existing LVLMs struggle to address these medical VQA problems effectively. Moreover, what surprises us is that medical-specialized LVLMs even exhibit inferior performance to those general-domain models, calling for a more versatile and robust LVLM in the biomedical field. The evaluation results not only reveal the current limitations of LVLM in understanding real medical images but also highlight our dataset's significance. Our code with dataset are available at https://github.com/OpenGVLab/Multi-Modality-Arena.

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arXiv2023

Enhancing Medical Task Performance in GPT-4V: A Comprehensive Study on Prompt Engineering Strategies

OpenAI's latest large vision-language model (LVLM), GPT-4V(ision), has piqued considerable interest for its potential in medical applications. Despite its promise, recent studies and internal reviews highlight its underperformance in specialized medical tasks. This paper explores the boundary of GPT-4V's capabilities in medicine, particularly in processing complex imaging data from endoscopies, CT scans, and MRIs etc. Leveraging open-source datasets, we assessed its foundational competencies, identifying substantial areas for enhancement. Our research emphasizes prompt engineering, an often-underutilized strategy for improving AI responsiveness. Through iterative testing, we refined the model's prompts, significantly improving its interpretative accuracy and relevance in medical imaging. From our comprehensive evaluations, we distilled 10 effective prompt engineering techniques, each fortifying GPT-4V's medical acumen. These methodical enhancements facilitate more reliable, precise, and clinically valuable insights from GPT-4V, advancing its operability in critical healthcare environments. Our findings are pivotal for those employing AI in medicine, providing clear, actionable guidance on harnessing GPT-4V's full diagnostic potential.

cs.CL↗

arXiv2023

SA-Med2D-20M Dataset: Segment Anything in 2D Medical Imaging with 20 Million masks

Segment Anything Model (SAM) has achieved impressive results for natural image segmentation with input prompts such as points and bounding boxes. Its success largely owes to massive labeled training data. However, directly applying SAM to medical image segmentation cannot perform well because SAM lacks medical knowledge -- it does not use medical images for training. To incorporate medical knowledge into SAM, we introduce SA-Med2D-20M, a large-scale segmentation dataset of 2D medical images built upon numerous public and private datasets. It consists of 4.6 million 2D medical images and 19.7 million corresponding masks, covering almost the whole body and showing significant diversity. This paper describes all the datasets collected in SA-Med2D-20M and details how to process these datasets. Furthermore, comprehensive statistics of SA-Med2D-20M are presented to facilitate the better use of our dataset, which can help the researchers build medical vision foundation models or apply their models to downstream medical applications. We hope that the large scale and diversity of SA-Med2D-20M can be leveraged to develop medical artificial intelligence for enhancing diagnosis, medical image analysis, knowledge sharing, and education. The data with the redistribution license is publicly available at https://github.com/OpenGVLab/SAM-Med2D.

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