Hanwen Xu

Sheng Zhang, Yanbo Xu, Naoto Usuyama et al. · cambridge, microsoft-research

Biomedical data is inherently multimodal, comprising physical measurements and natural language narratives. A generalist biomedical AI model needs to simultaneously process different modalities of data, including text and images. Therefore, training an effective generalist biomedical model requires high-quality multimodal data, such as parallel image-text pairs. Here, we present PMC-15M, a novel dataset that is two orders of magnitude larger than existing biomedical multimodal datasets such as MIMIC-CXR, and spans a diverse range of biomedical image types. PMC-15M contains 15 million biomedical image-text pairs collected from 4.4 million scientific articles. Based on PMC-15M, we have pretrained BiomedCLIP, a multimodal foundation model, with domain-specific adaptations tailored to biomedical vision-language processing. We conducted extensive experiments and ablation studies on standard biomedical imaging tasks from retrieval to classification to visual question-answering (VQA). BiomedCLIP achieved new state-of-the-art results in a wide range of standard datasets, substantially outperforming prior approaches. Intriguingly, by large-scale pretraining on diverse biomedical image types, BiomedCLIP even outperforms state-of-the-art radiology-specific models such as BioViL in radiology-specific tasks such as RSNA pneumonia detection. In summary, BiomedCLIP is a fully open-access foundation model that achieves state-of-the-art performance on various biomedical tasks, paving the way for transformative multimodal biomedical discovery and applications. We release our models at https://aka.ms/biomedclip to facilitate future research in multimodal biomedical AI.

Pengcheng Jiang, Jiacheng Lin, Zhiyi Shi et al. · stanford

Cutting-edge agentic AI systems are built on foundation models that can be adapted to plan, reason, and interact with external tools to perform increasingly complex and specialized tasks. As these systems grow in capability and scope, adaptation becomes a central mechanism for improving performance, reliability, and generalization. In this paper, we unify the rapidly expanding research landscape into a systematic framework that spans both agent adaptations and tool adaptations. We further decompose these into tool-execution-signaled and agent-output-signaled forms of agent adaptation, as well as agent-agnostic and agent-supervised forms of tool adaptation. We demonstrate that this framework helps clarify the design space of adaptation strategies in agentic AI, makes their trade-offs explicit, and provides practical guidance for selecting or switching among strategies during system design. We then review the representative approaches in each category, analyze their strengths and limitations, and highlight key open challenges and future opportunities. Overall, this paper aims to offer a conceptual foundation and practical roadmap for researchers and practitioners seeking to build more capable, efficient, and reliable agentic AI systems.

Daoyu Li, Hanwen Xu, Miao Cao et al.

Computational reconstruction plays a vital role in computer vision and computational photography. Most of the conventional optimization and deep learning techniques explore local information for reconstruction. Recently, nonlocal low-rank (NLR) reconstruction has achieved remarkable success in improving accuracy and generalization. However, the computational cost has inhibited NLR from seeking global structural similarity, which consequentially keeps it trapped in the tradeoff between accuracy and efficiency and prevents it from high-dimensional large-scale tasks. To address this challenge, we report here the global low-rank (GLR) optimization technique, realizing highly-efficient large-scale reconstruction with global self-similarity. Inspired by the self-attention mechanism in deep learning, GLR extracts exemplar image patches by feature detection instead of conventional uniform selection. This directly produces key patches using structural features to avoid burdensome computational redundancy. Further, it performs patch matching across the entire image via neural-based convolution, which produces the global similarity heat map in parallel, rather than conventional sequential block-wise matching. As such, GLR improves patch grouping efficiency by more than one order of magnitude. We experimentally demonstrate GLR's effectiveness on temporal, frequency, and spectral dimensions, including different computational imaging modalities of compressive temporal imaging, magnetic resonance imaging, and multispectral filter array demosaicing. This work presents the superiority of inherent fusion of deep learning strategies and iterative optimization, and breaks the persistent dilemma of the tradeoff between accuracy and efficiency for various large-scale reconstruction tasks.

Hanwen Xu, Xuyao Huang, Yuzhe Liu et al.

Large language model (LLM) agents have exhibited strong problem-solving competence across domains like research and coding. Yet, it remains underexplored whether LLM agents can tackle compounding real-world problems that require a diverse set of tools to complete. Given a broad, heterogeneous tool repository, LLM agents must not only select appropriate tools based on task planning analysis but also strategically schedule the execution order to ensure efficiency. This paper introduces TPS-Bench to benchmark the ability of LLM agents in solving such problems that demand Tool Planning and Scheduling. TPS-Bench collects 200 compounding tasks of two difficulty levels, based on a tool repository containing hundreds of model context protocol (MCP) tools. In particular, each task is composed of multiple subtasks, such as web search, map navigation, calendar checking, etc., and each subtask can be completed by a basic tool. Our evaluation emphasizes both task completion rate and efficiency. The empirical studies on popular closed-source and open-source LLMs indicate that most models can perform reasonable tool planning, but differ in scheduling. For example, GLM-4.5 achieves an outperforming task completion rate of 64.72% with extensive sequential tool calls, hence suffering from significantly long execution time. By contrast, GPT-4o prioritizes parallel tool calls but achieves only a 45.08% completion rate. Considering reinforcement learning (RL) can be a viable way to improve the scheduling efficiency without compromising performance, we perform an initial study on Qwen3-1.7B and witness a 14% reduction in execution time alongside a 6% gain in task completion rate based on rarely 100 RL training samples. Our code is available https://github.com/hanwenxu1/mcp-agent.

Zixuan Liu, Hanwen Xu, Addie Woicik et al.

We present OCTCube-M, a 3D OCT-based multi-modal foundation model for jointly analyzing OCT and en face images. OCTCube-M first developed OCTCube, a 3D foundation model pre-trained on 26,685 3D OCT volumes encompassing 1.62 million 2D OCT images. It then exploits a novel multi-modal contrastive learning framework COEP to integrate other retinal imaging modalities, such as fundus autofluorescence and infrared retinal imaging, into OCTCube, efficiently extending it into multi-modal foundation models. OCTCube achieves best performance on predicting 8 retinal diseases, demonstrating strong generalizability on cross-cohort, cross-device and cross-modality prediction. OCTCube can also predict cross-organ nodule malignancy (CT) and low cardiac ejection fraction as well as systemic diseases, such as diabetes and hypertension, revealing its wide applicability beyond retinal diseases. We further develop OCTCube-IR using COEP with 26,685 OCT and IR image pairs. OCTCube-IR can accurately retrieve between OCT and IR images, allowing joint analysis between 3D and 2D retinal imaging modalities. Finally, we trained a tri-modal foundation model OCTCube-EF from 4 million 2D OCT images and 400K en face retinal images. OCTCube-EF attains the best performance on predicting the growth rate of geographic atrophy (GA) across datasets collected from 6 multi-center global trials conducted in 23 countries. This improvement is statistically equivalent to running a clinical trial with more than double the size of the original study. Our analysis based on another retrospective case study reveals OCTCube-EF's ability to avoid false positive Phase-III results according to its accurate treatment effect estimation on the Phase-II results. In sum, OCTCube-M is a 3D multi-modal foundation model framework that integrates OCT and other retinal imaging modalities revealing substantial diagnostic and prognostic benefits.

Juan Manuel Zambrano Chaves, Shih-Cheng Huang, Yanbo Xu et al. · microsoft-research

The scaling laws and extraordinary performance of large foundation models motivate the development and utilization of such models in biomedicine. However, despite early promising results on some biomedical benchmarks, there are still major challenges that need to be addressed before these models can be used in real-world clinics. Frontier general-domain models such as GPT-4V still have significant performance gaps in multimodal biomedical applications. More importantly, less-acknowledged pragmatic issues, including accessibility, model cost, and tedious manual evaluation make it hard for clinicians to use state-of-the-art large models directly on private patient data. Here, we explore training open-source small multimodal models (SMMs) to bridge competency gaps for unmet clinical needs in radiology. To maximize data efficiency, we adopt a modular approach by incorporating state-of-the-art pre-trained models for image and text modalities, and focusing on training a lightweight adapter to ground each modality to the text embedding space, as exemplified by LLaVA-Med. For training, we assemble a large dataset of over 697 thousand radiology image-text pairs. For evaluation, we propose CheXprompt, a GPT-4-based metric for factuality evaluation, and demonstrate its parity with expert evaluation. For best practice, we conduct a systematic ablation study on various choices in data engineering and multimodal training. The resulting LlaVA-Rad (7B) model attains state-of-the-art results on standard radiology tasks such as report generation and cross-modal retrieval, even outperforming much larger models such as GPT-4V and Med-PaLM M (84B). The inference of LlaVA-Rad is fast and can be performed on a single V100 GPU in private settings, offering a promising state-of-the-art tool for real-world clinical applications.

Zequn Liu, Kefei Duan, Junwei Yang et al.

Heterogeneous Information Network (HIN) is essential to study complicated networks containing multiple edge types and node types. Meta-path, a sequence of node types and edge types, is the core technique to embed HINs. Since manually curating meta-paths is time-consuming, there is a pressing need to develop automated meta-path generation approaches. Existing meta-path generation approaches cannot fully exploit the rich textual information in HINs, such as node names and edge type names. To address this problem, we propose MetaFill, a text-infilling-based approach for meta-path generation. The key idea of MetaFill is to formulate meta-path identification problem as a word sequence infilling problem, which can be advanced by Pretrained Language Models (PLMs). We observed the superior performance of MetaFill against existing meta-path generation methods and graph embedding methods that do not leverage meta-paths in both link prediction and node classification on two real-world HIN datasets. We further demonstrated how MetaFill can accurately classify edges in the zero-shot setting, where existing approaches cannot generate any meta-paths. MetaFill exploits PLMs to generate meta-paths for graph embedding, opening up new avenues for language model applications in graph analysis.

Yifeng Liu, Hanwen Xu, Tangqi Fang et al.

As a fundamental task in computational chemistry, retrosynthesis prediction aims to identify a set of reactants to synthesize a target molecule. Existing template-free approaches only consider the graph structures of the target molecule, which often cannot generalize well to rare reaction types and large molecules. Here, we propose T-Rex, a text-assisted retrosynthesis prediction approach that exploits pre-trained text language models, such as ChatGPT, to assist the generation of reactants. T-Rex first exploits ChatGPT to generate a description for the target molecule and rank candidate reaction centers based both the description and the molecular graph. It then re-ranks these candidates by querying the descriptions for each reactants and examines which group of reactants can best synthesize the target molecule. We observed that T-Rex substantially outperformed graph-based state-of-the-art approaches on two datasets, indicating the effectiveness of considering text information. We further found that T-Rex outperformed the variant that only use ChatGPT-based description without the re-ranking step, demonstrate how our framework outperformed a straightforward integration of ChatGPT and graph information. Collectively, we show that text generated by pre-trained language models can substantially improve retrosynthesis prediction, opening up new avenues for exploiting ChatGPT to advance computational chemistry. And the codes can be found at https://github.com/lauyikfung/T-Rex.

Hanwen Xu, Jiayou Zhang, Zhirui Wang et al.

In the expansion of biomedical dataset, the same category may be labeled with different terms, thus being tedious and onerous to curate these terms. Therefore, automatically mapping synonymous terms onto the ontologies is desirable, which we name as biomedical synonym prediction task. Unlike biomedical concept normalization (BCN), no clues from context can be used to enhance synonym prediction, making it essential to extract graph features from ontology. We introduce an expert-curated dataset OBO-syn encompassing 70 different types of concepts and 2 million curated concept-term pairs for evaluating synonym prediction methods. We find BCN methods perform weakly on this task for not making full use of graph information. Therefore, we propose GraphPrompt, a prompt-based learning approach that creates prompt templates according to the graphs. GraphPrompt obtained 37.2\% and 28.5\% improvement on zero-shot and few-shot settings respectively, indicating the effectiveness of these graph-based prompt templates. We envision that our method GraphPrompt and OBO-syn dataset can be broadly applied to graph-based NLP tasks, and serve as the basis for analyzing diverse and accumulating biomedical data. All the data and codes are avalible at: https://github.com/HanwenXuTHU/GraphPrompt

Jiacheng Lin, Kun Qian, Arvind Srinivasan et al.

Personalization today is fundamentally platform-centric: services build user representations from the behavioral fragments they observe. Yet no platform can construct a complete picture of the user, as competitive incentives, legal constraints, user privacy concerns, and epistemic limits create persistent data barriers. This paper argues for a shift from platform-centric personalization to user-governed personalization, where only the user can integrate fragmented contexts across platforms and the offline world. The key asymmetry lies in data access: only users can aggregate their own cross-platform and offline information. Large language model (LLM) agents make such integration practically feasible for the first time by enabling reasoning over heterogeneous personal data and transforming users' cross-context information into actionable personalization capabilities. We provide proof-of-concept evidence that users equipped with cross-platform data exports and an off-the-shelf LLM agent can outperform single-platform personalization baselines. We conclude by outlining a research agenda for building scalable user-governed personalization systems.

Yongkang Li, Brian Wong, King Wai Chiu et al.

Chemical imaging enables label-free visualization of cells, tissues and living systems while providing direct biochemical information that is difficult to obtain with conventional fluorescence microscopy. Despite its promise in applications ranging from intraoperative diagnosis to drug-response analysis, its broader use remains limited by slow data acquisition, particularly for three-dimensional imaging. Here we present MicroDiffuse3D, a pretrained foundation model for 3D microscopy image restoration that recovers high-quality volumetric structure from degraded low-resolution measurements acquired at substantially higher throughput. We evaluated MicroDiffuse3D across three challenging restoration settings, including 3D super-resolution under 16-fold volumetric sparsity, joint degradation in resolution and noise, and 3D denoising in the low signal-to-noise ratio (SNR) regime, where the model delivered clear gains over strong baselines. Under the sparse 3D super-resolution setting, MicroDiffuse3D produced clearer continuity across depth with fewer artifacts and improved segmentation quality by 10.58% and line-profile concordance by 15.59%. Together, our results establish pretrained 3D restoration as a broadly applicable strategy for overcoming the throughput and SNR limitations in volumetric chemical imaging, enabling high-resolution analysis at scales and speeds that were previously difficult to achieve.

Wenhui Wang, Shuming Ma, Hanwen Xu et al.

This technical report presents LongViT, a vision Transformer that can process gigapixel images in an end-to-end manner. Specifically, we split the gigapixel image into a sequence of millions of patches and project them linearly into embeddings. LongNet is then employed to model the extremely long sequence, generating representations that capture both short-range and long-range dependencies. The linear computation complexity of LongNet, along with its distributed algorithm, enables us to overcome the constraints of both computation and memory. We apply LongViT in the field of computational pathology, aiming for cancer diagnosis and prognosis within gigapixel whole-slide images. Experimental results demonstrate that LongViT effectively encodes gigapixel images and outperforms previous state-of-the-art methods on cancer subtyping and survival prediction. Code and models will be available at https://aka.ms/LongViT.

Kunpeng Zhang, Hanwen Xu, Sheng Wang

Deciphering tumor microenvironment from Whole Slide Images (WSIs) is intriguing as it is key to cancer diagnosis, prognosis and treatment response. While these gigapixel images on one hand offer a comprehensive portrait of cancer, on the other hand, the extremely large size, as much as more than 10 billion pixels, make it challenging and time-consuming to navigate to corresponding regions to support diverse clinical inspection. Inspired by pathologists who conducted navigation on WSIs with a combination of sampling, reasoning and self-reflection, we proposed "PathReasoning", a multi-modal reasoning agent that iteratively navigates across WSIs through multiple rounds of reasoning and refinements. Specifically, starting with randomly sampled candidate regions, PathReasoning reviews current selections with self-reflection, reasoning over the correspondence between visual observations and clinical questions, and concludes by proposing new regions to explore. Across rounds, PathReasoning builds a reasoning chain that gradually directs attention to diagnostically relevant areas. PathReasoning turns each whole slide into a sequence of question-guided views, allowing the model to efficiently find informative ROIs within a fixed number of steps, without the need for dense pixel-level annotations. PathReasoning can substantially outperform strong ROI-selection approaches by 6.7% and 3.1% of AUROC on subtyping and longitudinal analysis tasks. The high-quality ROIs further support accurate report generation on breast cancer, significantly outperforming the standard GPT-4o by 10% in accuracy. PathReasoning prioritizes question-specific regions and constructs interpretable reasoning chains, supporting efficient slide review, consistent diagnostic interpretations, comprehensive reporting, and evidence traceability in digital pathology.

Jiacheng Lin, Hanwen Xu, Zifeng Wang et al.

Clinical trials are fundamental in developing new drugs, medical devices, and treatments. However, they are often time-consuming and have low success rates. Although there have been initial attempts to create large language models (LLMs) for clinical trial design and patient-trial matching, these models remain task-specific and not adaptable to diverse clinical trial tasks. To address this challenge, we propose a clinical trial foundation model named Panacea, designed to handle multiple tasks, including trial search, trial summarization, trial design, and patient-trial matching. We also assemble a large-scale dataset, named TrialAlign, of 793,279 trial documents and 1,113,207 trial-related scientific papers, to infuse clinical knowledge into the model by pre-training. We further curate TrialInstruct, which has 200,866 of instruction data for fine-tuning. These resources enable Panacea to be widely applicable for a range of clinical trial tasks based on user requirements. We evaluated Panacea on a new benchmark, named TrialPanorama, which covers eight clinical trial tasks. Our method performed the best on seven of the eight tasks compared to six cutting-edge generic or medicine-specific LLMs. Specifically, Panacea showed great potential to collaborate with human experts in crafting the design of eligibility criteria, study arms, and outcome measures, in multi-round conversations. In addition, Panacea achieved 14.42% improvement in patient-trial matching, 41.78% to 52.02% improvement in trial search, and consistently ranked at the top for five aspects of trial summarization. Our approach demonstrates the effectiveness of Panacea in clinical trials and establishes a comprehensive resource, including training data, model, and benchmark, for developing clinical trial foundation models, paving the path for AI-based clinical trial development.

Liheng Bian, Daoyu Li, Shuoguang Wang et al.

Millimeter-wave (MMW) imaging is emerging as a promising technique for safe security inspection. It achieves a delicate balance between imaging resolution, penetrability and human safety, resulting in higher resolution compared to low-frequency microwave, stronger penetrability compared to visible light, and stronger safety compared to X ray. Despite of recent advance in the last decades, the high cost of requisite large-scale antenna array hinders widespread adoption of MMW imaging in practice. To tackle this challenge, we report a large-scale single-shot MMW imaging framework using sparse antenna array, achieving low-cost but high-fidelity security inspection under an interpretable learning scheme. We first collected extensive full-sampled MMW echoes to study the statistical ranking of each element in the large-scale array. These elements are then sampled based on the ranking, building the experimentally optimal sparse sampling strategy that reduces the cost of antenna array by up to one order of magnitude. Additionally, we derived an untrained interpretable learning scheme, which realizes robust and accurate image reconstruction from sparsely sampled echoes. Last, we developed a neural network for automatic object detection, and experimentally demonstrated successful detection of concealed centimeter-sized targets using 10% sparse array, whereas all the other contemporary approaches failed at the same sample sampling ratio. The performance of the reported technique presents higher than 50% superiority over the existing MMW imaging schemes on various metrics including precision, recall, and mAP50. With such strong detection ability and order-of-magnitude cost reduction, we anticipate that this technique provides a practical way for large-scale single-shot MMW imaging, and could advocate its further practical applications.

Habiba Farrukh, Tinghan Yang, Hanwen Xu et al.

With smart devices being an essential part of our everyday lives, unsupervised access to the mobile sensors' data can result in a multitude of side-channel attacks. In this paper, we study potential data leaks from Apple Pencil (2nd generation) supported by the Apple iPad Pro, the latest stylus pen which attaches to the iPad body magnetically for charging. We observe that the Pencil's body affects the magnetic readings sensed by the iPad's magnetometer when a user is using the Pencil. Therefore, we ask: Can we infer what a user is writing on the iPad screen with the Apple Pencil, given access to only the iPad's motion sensors' data? To answer this question, we present Side-channel attack on Stylus pencil through Sensors (S3), a system that identifies what a user is writing from motion sensor readings. We first use the sharp fluctuations in the motion sensors' data to determine when a user is writing on the iPad. We then introduce a high-dimensional particle filter to track the location and orientation of the Pencil during usage. Lastly, to guide particles, we build the Pencil's magnetic map serving as a bridge between the measured magnetic data and the Pencil location and orientation. We evaluate S3 with 10 subjects and demonstrate that we correctly identify 93.9%, 96%, 97.9%, and 93.33% of the letters, numbers, shapes, and words by only having access to the motion sensors' data.