Jiajun Cheng

Xuanzhao Dong, Wenhui Zhu, Xiwen Chen et al.

The advancement of general medical Multimodal Large Language Models (MLLMs) has shown great potential for building conversational assistants to support clinical diagnosis. However, their adaptation to highly specialized domains such as ophthalmology remains underexplored, primarily due to the scarcity of large-scale, domain-specific instruction-tuning data. Existing ophthalmic datasets for conversational agents are often limited in scale and largely rely on images from established public benchmarks, limiting the scalability of ophthalmic MLLMs and their ability to capture real-world clinical complexity. To address this gap, we propose $\textbf{OphIn-Engine}$, an ophthalmology-specific instruction data curation pipeline that constructs high-quality instruction data from open-access ophthalmology web-scale videos. The pipeline integrates multimodal transcription for extracting image-transcript pairs, visual cue separation and scoring for identifying clinically relevant visual descriptions, and instruction synthesis with quality control for generating accurate and diverse clinical dialogues. Using this engine, we introduce $\textbf{OphIn-500K}$, a large-scale multimodal ophthalmology instruction-tuning dataset containing over 500,000 instruction instances and more than 151,000 unique images from over 29,000 video clips, formatted as visual question answering (VQA), multi-turn conversational interactions, and chain-of-thought (CoT) reasoning. Built upon this dataset, we further develop $\textbf{OphIn-VL}$, an ophthalmology-specific MLLM with advanced visual understanding and conversational capabilities. Comprehensive experiments and case studies demonstrate that OphIn-VL achieves superior performance compared with state-of-the-art general medical and domain-specific MLLMs.

Xuanzhao Dong, Wenhui Zhu, Xiwen Chen et al.

Over the past decade, generative models have demonstrated success in enhancing fundus images. However, the evaluation of these models remains a challenge. A benchmark for fundus image enhancement is needed for three main reasons:(1) Conventional denoising metrics such as PSNR and SSIM fail to capture clinically relevant features, such as lesion preservation and vessel morphology consistency, limiting their applicability in real-world settings; (2) There is a lack of unified evaluation protocols that address both paired and unpaired enhancement methods, particularly those guided by clinical expertise; and (3) An evaluation framework should provide actionable insights to guide future advancements in clinically aligned enhancement models. To address these gaps, we introduce EyeBench-V2, a benchmark designed to bridge the gap between enhancement model performance and clinical utility. Our work offers three key contributions:(1) Multi-dimensional clinical-alignment through downstream evaluations: Beyond standard enhancement metrics, we assess performance across clinically meaningful tasks including vessel segmentation, diabetic retinopathy (DR) grading, generalization to unseen noise patterns, and lesion segmentation. (2) Expert-guided evaluation design: We curate a novel dataset enabling fair comparisons between paired and unpaired enhancement methods, accompanied by a structured manual assessment protocol by medical experts, which evaluates clinically critical aspects such as lesion structure alterations, background color shifts, and the introduction of artificial structures. (3) Actionable insights: Our benchmark provides a rigorous, task-oriented analysis of existing generative models, equipping clinical researchers with the evidence needed to make informed decisions, while also identifying limitations in current methods to inform the design of next-generation enhancement models.

Xuanzhao Dong, Wenhui Zhu, Yujian Xiong et al.

Color fundus photography (CFP) is central to diagnosing and monitoring retinal disease, yet its acquisition variability (e.g., illumination changes) often degrades image quality, which motivates robust enhancement methods. Unpaired enhancement pipelines are typically GAN-based, however, they can distort clinically critical vasculature, altering vessel topology and endpoint integrity. Motivated by these structural alterations, we propose Vessel-Aware Optimal Transport (\textbf{VAOT}), a framework that combines an optimal-transport objective with two structure-preserving regularizers: (i) a skeleton-based loss to maintain global vascular connectivity and (ii) an endpoint-aware loss to stabilize local termini. These constraints guide learning in the unpaired setting, reducing noise while preserving vessel structure. Experimental results on synthetic degradation benchmark and downstream evaluations in vessel and lesion segmentation demonstrate the superiority of the proposed methods against several state-of-the art baselines. The code is available at https://github.com/Retinal-Research/VAOT

Lin Huang, Arthur Jiang, XiaoLi Liu et al.

All-atom molecular simulation serves as a quintessential ``computational microscope'' for understanding the machinery of life, yet it remains fundamentally limited by the trade-off between quantum-mechanical (QM) accuracy and biological scale. We present UBio-MolFM, a universal foundation model framework specifically engineered to bridge this gap. UBio-MolFM introduces three synergistic innovations: (1) UBio-Mol26, a large bio-specific dataset constructed via a multi-fidelity ``Two-Pronged Strategy'' that combines systematic bottom-up enumeration with top-down sampling of native protein environments (up to 1,200 atoms); (2) E2Former-V2, a linear-scaling equivariant transformer that integrates Equivariant Axis-Aligned Sparsification (EAAS) and Long-Short Range (LSR) modeling to capture non-local physics with up to ~4x higher inference throughput in our large-system benchmarks; and (3) a Three-Stage Curriculum Learning protocol that transitions from energy initialization to energy-force consistency, with force-focused supervision to mitigate energy offsets. Rigorous benchmarking across microscopic forces and macroscopic observables -- including liquid water structure, ionic solvation, and peptide folding -- demonstrates that UBio-MolFM achieves ab initio-level fidelity on large, out-of-distribution biomolecular systems (up to ~1,500 atoms) and realistic MD observables. By reconciling scalability with quantum precision, UBio-MolFM provides a robust, ready-to-use tool for the next generation of computational biology.

Anirudh Rayas, Jiajun Cheng, Rajasekhar Anguluri et al.

Complex networked systems driven by latent inputs are common in fields like neuroscience, finance, and engineering. A key inference problem here is to learn edge connectivity from node outputs (potentials). We focus on systems governed by steady-state linear conservation laws: $X_t = {L^{\ast}}Y_{t}$, where $X_t, Y_t \in \mathbb{R}^p$ denote inputs and potentials, respectively, and the sparsity pattern of the $p \times p$ Laplacian $L^{\ast}$ encodes the edge structure. Assuming $X_t$ to be a wide-sense stationary stochastic process with a known spectral density matrix, we learn the support of $L^{\ast}$ from temporally correlated samples of $Y_t$ via an $\ell_1$-regularized Whittle's maximum likelihood estimator (MLE). The regularization is particularly useful for learning large-scale networks in the high-dimensional setting where the network size $p$ significantly exceeds the number of samples $n$. We show that the MLE problem is strictly convex, admitting a unique solution. Under a novel mutual incoherence condition and certain sufficient conditions on $(n, p, d)$, we show that the ML estimate recovers the sparsity pattern of $L^\ast$ with high probability, where $d$ is the maximum degree of the graph underlying $L^{\ast}$. We provide recovery guarantees for $L^\ast$ in element-wise maximum, Frobenius, and operator norms. Finally, we complement our theoretical results with several simulation studies on synthetic and benchmark datasets, including engineered systems (power and water networks), and real-world datasets from neural systems (such as the human brain).

Jiajun Cheng, Xiaofan Yu, Subarna et al.

Recognizing instruments' interactions with tissues is essential for building context-aware AI assistants in robotic surgery. Vision-language models (VLMs) have opened a new avenue for surgical perception and achieved better generalization on a wide range of tasks compared to conventional task-specific deep learning approaches. However, their performance on instrument--tissue interaction recognition remains limited, largely due to two challenges: (1) many models do not effectively leverage temporal information, and (2) alignment between vision and text often misses fine-grained action details. To address these issues, we propose TrajPred, a framework that encodes instrument trajectories to incorporate temporal motion cues and, conditioned on these trajectories, introduces a predictor module to generate visual semantic embeddings that better capture fine-grained action details. We further incorporate prompt tuning and a verb-rephrasing technique to enable smooth adaptation to the instrument--tissue interaction recognition task. Extensive experiments on the public laparoscopic benchmark, CholecT50, show that our method improves both Average Precision and Top-K accuracy. We also investigate whether visual embeddings of instrument--tissue interaction regions align better with the corresponding text by visualizing the cosine similarity between visual and textual embeddings. The visualization results indicate that the proposed method improves alignment between relevant visual and textual representations.