arXiv subjects

Junjun He

Publications and source records attributed to Junjun He.

At least 55 records · Page 3Linked to original sources

arXiv2025

SciReasoner: Laying the Scientific Reasoning Ground Across Disciplines

We present a scientific reasoning foundation model that aligns natural language with heterogeneous scientific representations. The model is pretrained on a 206B-token corpus spanning scientific text, pure sequences, and sequence-text pairs, then aligned via SFT on 40M instructions, annealed cold-start bootstrapping to elicit long-form chain-of-thought, and reinforcement learning with task-specific reward shaping, which instills deliberate scientific reasoning. It supports four capability families, covering up to 103 tasks across workflows: (i) faithful translation between text and scientific formats, (ii) text/knowledge extraction, (iii) property prediction, (iv) property classification, (v) unconditional and conditional sequence generation and design. Compared with specialist systems, our approach broadens instruction coverage, improves cross-domain generalization, and enhances fidelity. We detail data curation and training and show that cross-discipline learning strengthens transfer and downstream reliability. The model, instruct tuning datasets and the evaluation code are open-sourced at https://huggingface.co/SciReason and https://github.com/open-sciencelab/SciReason.

cs.CL↗

arXiv2025

HyperST: Hierarchical Hyperbolic Learning for Spatial Transcriptomics Prediction

Spatial Transcriptomics (ST) merges the benefits of pathology images and gene expression, linking molecular profiles with tissue structure to analyze spot-level function comprehensively. Predicting gene expression from histology images is a cost-effective alternative to expensive ST technologies. However, existing methods mainly focus on spot-level image-to-gene matching but fail to leverage the full hierarchical structure of ST data, especially on the gene expression side, leading to incomplete image-gene alignment. Moreover, a challenge arises from the inherent information asymmetry: gene expression profiles contain more molecular details that may lack salient visual correlates in histological images, demanding a sophisticated representation learning approach to bridge this modality gap. We propose HyperST, a framework for ST prediction that learns multi-level image-gene representations by modeling the data's inherent hierarchy within hyperbolic space, a natural geometric setting for such structures. First, we design a Multi-Level Representation Extractors to capture both spot-level and niche-level representations from each modality, providing context-aware information beyond individual spot-level image-gene pairs. Second, a Hierarchical Hyperbolic Alignment module is introduced to unify these representations, performing spatial alignment while hierarchically structuring image and gene embeddings. This alignment strategy enriches the image representations with molecular semantics, significantly improving cross-modal prediction. HyperST achieves state-of-the-art performance on four public datasets from different tissues, paving the way for more scalable and accurate spatial transcriptomics prediction.

cs.CV↗

arXiv2025

Scaling Tumor Segmentation: Best Lessons from Real and Synthetic Data

AI for tumor segmentation is limited by the lack of large, voxel-wise annotated datasets, which are hard to create and require medical experts. In our proprietary JHH dataset of 3,000 annotated pancreatic tumor scans, we found that AI performance stopped improving after 1,500 scans. With synthetic data, we reached the same performance using only 500 real scans. This finding suggests that synthetic data can steepen data scaling laws, enabling more efficient model training than real data alone. Motivated by these lessons, we created AbdomenAtlas 2.0--a dataset of 10,135 CT scans with a total of 15,130 tumor instances per-voxel manually annotated in six organs (pancreas, liver, kidney, colon, esophagus, and uterus) and 5,893 control scans. Annotated by 23 expert radiologists, it is several orders of magnitude larger than existing public tumor datasets. While we continue expanding the dataset, the current version of AbdomenAtlas 2.0 already provides a strong foundation--based on lessons from the JHH dataset--for training AI to segment tumors in six organs. It achieves notable improvements over public datasets, with a +7% DSC gain on in-distribution tests and +16% on out-of-distribution tests.

cs.CV↗

arXiv2025

From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery

Artificial intelligence (AI) is reshaping scientific discovery, evolving from specialized computational tools into autonomous research partners. We position Agentic Science as a pivotal stage within the broader AI for Science paradigm, where AI systems progress from partial assistance to full scientific agency. Enabled by large language models (LLMs), multimodal systems, and integrated research platforms, agentic AI shows capabilities in hypothesis generation, experimental design, execution, analysis, and iterative refinement -- behaviors once regarded as uniquely human. This survey provides a domain-oriented review of autonomous scientific discovery across life sciences, chemistry, materials science, and physics. We unify three previously fragmented perspectives -- process-oriented, autonomy-oriented, and mechanism-oriented -- through a comprehensive framework that connects foundational capabilities, core processes, and domain-specific realizations. Building on this framework, we (i) trace the evolution of AI for Science, (ii) identify five core capabilities underpinning scientific agency, (iii) model discovery as a dynamic four-stage workflow, (iv) review applications across the above domains, and (v) synthesize key challenges and future opportunities. This work establishes a domain-oriented synthesis of autonomous scientific discovery and positions Agentic Science as a structured paradigm for advancing AI-driven research.

cs.LG↗

arXiv2025

HealthFlow: A Self-Evolving AI Agent with Meta Planning for Autonomous Healthcare Research

The rapid proliferation of scientific knowledge presents a grand challenge: transforming this vast repository of information into an active engine for discovery, especially in high-stakes domains like healthcare. Current AI agents, however, are constrained by static, predefined strategies, limiting their ability to navigate the complex, evolving ecosystem of scientific research. This paper introduces HealthFlow, a self-evolving AI agent that overcomes this limitation through a novel meta-level evolution mechanism. HealthFlow autonomously refines its high-level problem-solving policies by distilling procedural successes and failures into a durable, structured knowledge base, enabling it to learn not just how to use tools, but how to strategize. To anchor our research and provide a community resource, we introduce EHRFlowBench, a new benchmark featuring complex health data analysis tasks systematically derived from peer-reviewed scientific literature. Our experiments demonstrate that HealthFlow's self-evolving approach significantly outperforms state-of-the-art agent frameworks. This work offers a new paradigm for intelligent systems that can learn to operationalize the procedural knowledge embedded in scientific content, marking a critical step toward more autonomous and effective AI for healthcare scientific discovery.

cs.AI↗

arXiv2025

Lumina-DiMOO: An Omni Diffusion Large Language Model for Multi-Modal Generation and Understanding

We introduce Lumina-DiMOO, an open-source foundational model for seamless multi-modal generation and understanding. Lumina-DiMOO sets itself apart from prior unified models by utilizing a fully discrete diffusion modeling to handle inputs and outputs across various modalities. This innovative approach allows Lumina-DiMOO to achieve higher sampling efficiency compared to previous autoregressive (AR) or hybrid AR-Diffusion paradigms and adeptly support a broad spectrum of multi-modal tasks, including text-to-image generation, image-to-image generation (e.g., image editing, subject-driven generation, and image inpainting, etc.), as well as image understanding. Lumina-DiMOO achieves state-of-the-art performance on multiple benchmarks, surpassing existing open-source unified multi-modal models. To foster further advancements in multi-modal and discrete diffusion model research, we release our code and checkpoints to the community. Project Page: https://synbol.github.io/Lumina-DiMOO.

cs.CV↗

arXiv2025

MedQ-Bench: Evaluating and Exploring Medical Image Quality Assessment Abilities in MLLMs

Medical Image Quality Assessment (IQA) serves as the first-mile safety gate for clinical AI, yet existing approaches remain constrained by scalar, score-based metrics and fail to reflect the descriptive, human-like reasoning process central to expert evaluation. To address this gap, we introduce MedQ-Bench, a comprehensive benchmark that establishes a perception-reasoning paradigm for language-based evaluation of medical image quality with Multi-modal Large Language Models (MLLMs). MedQ-Bench defines two complementary tasks: (1) MedQ-Perception, which probes low-level perceptual capability via human-curated questions on fundamental visual attributes; and (2) MedQ-Reasoning, encompassing both no-reference and comparison reasoning tasks, aligning model evaluation with human-like reasoning on image quality. The benchmark spans five imaging modalities and over forty quality attributes, totaling 2,600 perceptual queries and 708 reasoning assessments, covering diverse image sources including authentic clinical acquisitions, images with simulated degradations via physics-based reconstructions, and AI-generated images. To evaluate reasoning ability, we propose a multi-dimensional judging protocol that assesses model outputs along four complementary axes. We further conduct rigorous human-AI alignment validation by comparing LLM-based judgement with radiologists. Our evaluation of 14 state-of-the-art MLLMs demonstrates that models exhibit preliminary but unstable perceptual and reasoning skills, with insufficient accuracy for reliable clinical use. These findings highlight the need for targeted optimization of MLLMs in medical IQA. We hope that MedQ-Bench will catalyze further exploration and unlock the untapped potential of MLLMs for medical image quality evaluation.

cs.CV↗

arXiv2025

Multimodal Medical Image Binding via Shared Text Embeddings

Medical image analysis increasingly relies on the integration of multiple imaging modalities to capture complementary anatomical and functional information, enabling more accurate diagnosis and treatment planning. Achieving aligned feature representations across these diverse modalities is therefore important for effective multimodal analysis. While contrastive language-image pre-training (CLIP) and its variant have enabled image-text alignments, they require explicitly paired data between arbitrary two modalities, which is difficult to acquire in medical contexts. To address the gap, we present Multimodal Medical Image Binding with Text (M\textsuperscript{3}Bind), a novel pre-training framework that enables seamless alignment of multiple medical imaging modalities through a shared text representation space without requiring explicit paired data between any two medical image modalities. Specifically, based on the insight that different images can naturally bind with text, M\textsuperscript{3}Bind first fine-tunes pre-trained CLIP-like image-text models to align their modality-specific text embedding space while preserving their original image-text alignments. Subsequently, we distill these modality-specific text encoders into a unified model, creating a shared text embedding space. Experiments on X-ray, CT, retina, ECG, and pathological images on multiple downstream tasks demonstrate that M\textsuperscript{3}Bind achieves state-of-the-art performance in zero-shot, few-shot classification and cross-modal retrieval tasks compared to its CLIP-like counterparts. These results validate M\textsuperscript{3}Bind's effectiveness in achieving cross-image-modal alignment for medical analysis.

eess.IV↗

arXiv2025

Towards Interpretable Counterfactual Generation via Multimodal Autoregression

Counterfactual medical image generation enables clinicians to explore clinical hypotheses, such as predicting disease progression, facilitating their decision-making. While existing methods can generate visually plausible images from disease progression prompts, they produce silent predictions that lack interpretation to verify how the generation reflects the hypothesized progression -- a critical gap for medical applications that require traceable reasoning. In this paper, we propose Interpretable Counterfactual Generation (ICG), a novel task requiring the joint generation of counterfactual images that reflect the clinical hypothesis and interpretation texts that outline the visual changes induced by the hypothesis. To enable ICG, we present ICG-CXR, the first dataset pairing longitudinal medical images with hypothetical progression prompts and textual interpretations. We further introduce ProgEmu, an autoregressive model that unifies the generation of counterfactual images and textual interpretations. We demonstrate the superiority of ProgEmu in generating progression-aligned counterfactuals and interpretations, showing significant potential in enhancing clinical decision support and medical education. Project page: https://progemu.github.io.

eess.IV↗

arXiv2025

InternVL3.5: Advancing Open-Source Multimodal Models in Versatility, Reasoning, and Efficiency

We introduce InternVL 3.5, a new family of open-source multimodal models that significantly advances versatility, reasoning capability, and inference efficiency along the InternVL series. A key innovation is the Cascade Reinforcement Learning (Cascade RL) framework, which enhances reasoning through a two-stage process: offline RL for stable convergence and online RL for refined alignment. This coarse-to-fine training strategy leads to substantial improvements on downstream reasoning tasks, e.g., MMMU and MathVista. To optimize efficiency, we propose a Visual Resolution Router (ViR) that dynamically adjusts the resolution of visual tokens without compromising performance. Coupled with ViR, our Decoupled Vision-Language Deployment (DvD) strategy separates the vision encoder and language model across different GPUs, effectively balancing computational load. These contributions collectively enable InternVL3.5 to achieve up to a +16.0\% gain in overall reasoning performance and a 4.05$\times$ inference speedup compared to its predecessor, i.e., InternVL3. In addition, InternVL3.5 supports novel capabilities such as GUI interaction and embodied agency. Notably, our largest model, i.e., InternVL3.5-241B-A28B, attains state-of-the-art results among open-source MLLMs across general multimodal, reasoning, text, and agentic tasks -- narrowing the performance gap with leading commercial models like GPT-5. All models and code are publicly released.

cs.CV↗

arXiv2025

Intern-S1: A Scientific Multimodal Foundation Model

In recent years, a plethora of open-source foundation models have emerged, achieving remarkable progress in some widely attended fields, with performance being quite close to that of closed-source models. However, in high-value but more challenging scientific professional fields, either the fields still rely on expert models, or the progress of general foundation models lags significantly compared to those in popular areas, far from sufficient for transforming scientific research and leaving substantial gap between open-source models and closed-source models in these scientific domains. To mitigate this gap and explore a step further toward Artificial General Intelligence (AGI), we introduce Intern-S1, a specialized generalist equipped with general understanding and reasoning capabilities with expertise to analyze multiple science modal data. Intern-S1 is a multimodal Mixture-of-Experts (MoE) model with 28 billion activated parameters and 241 billion total parameters, continually pre-trained on 5T tokens, including over 2.5T tokens from scientific domains. In the post-training stage, Intern-S1 undergoes offline and then online reinforcement learning (RL) in InternBootCamp, where we propose Mixture-of-Rewards (MoR) to synergize the RL training on more than 1000 tasks simultaneously. Through integrated innovations in algorithms, data, and training systems, Intern-S1 achieved top-tier performance in online RL training. On comprehensive evaluation benchmarks, Intern-S1 demonstrates competitive performance on general reasoning tasks among open-source models and significantly outperforms open-source models in scientific domains, surpassing closed-source state-of-the-art models in professional tasks, such as molecular synthesis planning, reaction condition prediction, predicting thermodynamic stabilities for crystals. Our models are available at https://huggingface.co/internlm/Intern-S1.

cs.LG↗

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

EventRR: Event Referential Reasoning for Referring Video Object Segmentation

Referring Video Object Segmentation (RVOS) aims to segment out the object in a video referred by an expression. Current RVOS methods view referring expressions as unstructured sequences, neglecting their crucial semantic structure essential for referent reasoning. Besides, in contrast to image-referring expressions whose semantics focus only on object attributes and object-object relations, video-referring expressions also encompass event attributes and event-event temporal relations. This complexity challenges traditional structured reasoning image approaches. In this paper, we propose the Event Referential Reasoning (EventRR) framework. EventRR decouples RVOS into object summarization part and referent reasoning part. The summarization phase begins by summarizing each frame into a set of bottleneck tokens, which are then efficiently aggregated in the video-level summarization step to exchange the global cross-modal temporal context. For reasoning part, EventRR extracts semantic eventful structure of a video-referring expression into highly expressive Referential Event Graph (REG), which is a single-rooted directed acyclic graph. Guided by topological traversal of REG, we propose Temporal Concept-Role Reasoning (TCRR) to accumulate the referring score of each temporal query from REG leaf nodes to root node. Each reasoning step can be interpreted as a question-answer pair derived from the concept-role relations in REG. Extensive experiments across four widely recognized benchmark datasets, show that EventRR quantitatively and qualitatively outperforms state-of-the-art RVOS methods. Code is available at https://github.com/bio-mlhui/EventRR

cs.CV↗

arXiv2025

ADAgent: LLM Agent for Alzheimer's Disease Analysis with Collaborative Coordinator

Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disease. Early and precise diagnosis of AD is crucial for timely intervention and treatment planning to alleviate the progressive neurodegeneration. However, most existing methods rely on single-modality data, which contrasts with the multifaceted approach used by medical experts. While some deep learning approaches process multi-modal data, they are limited to specific tasks with a small set of input modalities and cannot handle arbitrary combinations. This highlights the need for a system that can address diverse AD-related tasks, process multi-modal or missing input, and integrate multiple advanced methods for improved performance. In this paper, we propose ADAgent, the first specialized AI agent for AD analysis, built on a large language model (LLM) to address user queries and support decision-making. ADAgent integrates a reasoning engine, specialized medical tools, and a collaborative outcome coordinator to facilitate multi-modal diagnosis and prognosis tasks in AD. Extensive experiments demonstrate that ADAgent outperforms SOTA methods, achieving significant improvements in accuracy, including a 2.7% increase in multi-modal diagnosis, a 0.7% improvement in multi-modal prognosis, and enhancements in MRI and PET diagnosis tasks.

eess.IV↗

arXiv2025

THE-Tree: Can Tracing Historical Evolution Enhance Scientific Verification and Reasoning?

Large Language Models (LLMs) are accelerating scientific idea generation, but rigorously evaluating these numerous, often superficial, AI-generated propositions for novelty and factual accuracy is a critical bottleneck; manual verification is too slow. Existing validation methods are inadequate: LLMs as standalone verifiers may hallucinate and lack domain knowledge (our findings show 60% unawareness of relevant papers in specific domains), while traditional citation networks lack explicit causality and narrative surveys are unstructured. This underscores a core challenge: the absence of structured, verifiable, and causally-linked historical data of scientific evolution.To address this,we introduce \textbf{THE-Tree} (\textbf{T}echnology \textbf{H}istory \textbf{E}volution Tree), a computational framework that constructs such domain-specific evolution trees from scientific literature. THE-Tree employs a search algorithm to explore evolutionary paths. During its node expansion, it utilizes a novel "Think-Verbalize-Cite-Verify" process: an LLM proposes potential advancements and cites supporting literature. Critically, each proposed evolutionary link is then validated for logical coherence and evidential support by a recovered natural language inference mechanism that interrogates the cited literature, ensuring that each step is grounded. We construct and validate 88 THE-Trees across diverse domains and release a benchmark dataset including up to 71k fact verifications covering 27k papers to foster further research. Experiments demonstrate that i) in graph completion, our THE-Tree improves hit@1 by 8% to 14% across multiple models compared to traditional citation networks; ii) for predicting future scientific developments, it improves hit@1 metric by nearly 10%; and iii) when combined with other methods, it boosts the performance of evaluating important scientific papers by almost 100%.

cs.AI↗

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.

eess.IV↗

arXiv2025

Ophora: A Large-Scale Data-Driven Text-Guided Ophthalmic Surgical Video Generation Model

In ophthalmic surgery, developing an AI system capable of interpreting surgical videos and predicting subsequent operations requires numerous ophthalmic surgical videos with high-quality annotations, which are difficult to collect due to privacy concerns and labor consumption. Text-guided video generation (T2V) emerges as a promising solution to overcome this issue by generating ophthalmic surgical videos based on surgeon instructions. In this paper, we present Ophora, a pioneering model that can generate ophthalmic surgical videos following natural language instructions. To construct Ophora, we first propose a Comprehensive Data Curation pipeline to convert narrative ophthalmic surgical videos into a large-scale, high-quality dataset comprising over 160K video-instruction pairs, Ophora-160K. Then, we propose a Progressive Video-Instruction Tuning scheme to transfer rich spatial-temporal knowledge from a T2V model pre-trained on natural video-text datasets for privacy-preserved ophthalmic surgical video generation based on Ophora-160K. Experiments on video quality evaluation via quantitative analysis and ophthalmologist feedback demonstrate that Ophora can generate realistic and reliable ophthalmic surgical videos based on surgeon instructions. We also validate the capability of Ophora for empowering downstream tasks of ophthalmic surgical workflow understanding. Code is available at https://github.com/uni-medical/Ophora.

eess.IV↗

arXiv2025

MedAide: Information Fusion and Anatomy of Medical Intents via LLM-based Agent Collaboration

In healthcare intelligence, the ability to fuse heterogeneous, multi-intent information from diverse clinical sources is fundamental to building reliable decision-making systems. Large Language Model (LLM)-driven information interaction systems currently showing potential promise in the healthcare domain. Nevertheless, they often suffer from information redundancy and coupling when dealing with complex medical intents, leading to severe hallucinations and performance bottlenecks. To this end, we propose MedAide, an LLM-based medical multi-agent collaboration framework designed to enable intent-aware information fusion and coordinated reasoning across specialized healthcare domains. Specifically, we introduce a regularization-guided module that combines syntactic constraints with retrieval augmented generation to decompose complex queries into structured representations, facilitating fine-grained clinical information fusion and intent resolution. Additionally, a dynamic intent prototype matching module is proposed to utilize dynamic prototype representation with a semantic similarity matching mechanism to achieve adaptive recognition and updating of the agent's intent in multi-round healthcare dialogues. Ultimately, we design a rotation agent collaboration mechanism that introduces dynamic role rotation and decision-level information fusion across specialized medical agents. Extensive experiments are conducted on four medical benchmarks with composite intents. Experimental results from automated metrics and expert doctor evaluations show that MedAide outperforms current LLMs and improves their medical proficiency and strategic reasoning.

cs.CL↗