Sheng Wang

Haozhe Zhao, Zefan Cai, Shuzheng Si et al. · pku, stanford

Since the resurgence of deep learning, vision-language models (VLMs) enhanced by large language models (LLMs) have grown exponentially in popularity. However, while LLMs can utilize extensive background knowledge and task information with in-context learning, most VLMs still struggle with understanding complex multi-modal prompts with multiple images, making VLMs less effective in downstream vision-language tasks. In this paper, we address the limitation above by 1) introducing vision-language Model with Multi-Modal In-Context Learning(MMICL), a new approach to allow the VLM to deal with multi-modal inputs efficiently; 2) proposing a novel context scheme to augment the in-context learning ability of the VLM; 3) constructing the Multi-modal In-Context Learning (MIC) dataset, designed to enhance the VLM's ability to understand complex multi-modal prompts. Our experiments confirm that MMICL achieves new state-of-the-art zero-shot performance on a wide range of general vision-language tasks, especially for complex benchmarks, including MME and MMBench. Our analysis demonstrates that MMICL effectively tackles the challenge of complex multi-modal prompt understanding and emerges the impressive ICL ability. Furthermore, we observe that MMICL successfully alleviates language bias in VLMs, a common issue for VLMs that often leads to hallucination when faced with extensive textual context. Our code, dataset, dataset tool, and model are available at https://github.com/PKUnlp-icler/MIC

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.

Jingqi Zhou, Sheng Wang, Dezhao Deng et al.

LLM-powered agentic systems excel at complex long-horizon tasks, but remain constrained by static configurations fixed before execution. Such rigidity forces a trade-off between domain-specific performance and cross-task generalization: strong priors and compact tool spaces aid specialization but weaken transfer, while task-agnostic workflows and broad action spaces expand coverage but dilute guidance. Existing pre-execution optimization, planner-worker orchestration, and configuration patching fall short of resolving this tension, as they decouple adaptation from execution, causing information loss, fragmented optimization, and ambiguous credit assignment. We propose ToolSelf, a tool-driven runtime self-reconfiguration paradigm that abstracts configuration updates as a standardized tool interface and unifies execution and adaptation within one policy's action space. The execution agent can dynamically update sub-goals, strategies, toolboxes, context, and context-management modes based on task progress and feedback. We further introduce Configuration-Aware Two-stage Training (CAT), which combines rejection sampling fine-tuning with trajectory-level KTO reinforcement learning to internalize self-reconfiguration. Across diverse benchmarks, zero-shot ToolSelf rivals task-specialized agents; after CAT training, ToolSelf gains 28.8 points over the static-configuration baseline on average, illuminating a path toward emergent adaptivity that obviates manually injected guidance.

Yue Guo, Wei Qiu, Gondy Leroy et al. · uw

Recent lay language generation systems have used Transformer models trained on a parallel corpus to increase health information accessibility. However, the applicability of these models is constrained by the limited size and topical breadth of available corpora. We introduce CELLS, the largest (63k pairs) and broadest-ranging (12 journals) parallel corpus for lay language generation. The abstract and the corresponding lay language summary are written by domain experts, assuring the quality of our dataset. Furthermore, qualitative evaluation of expert-authored plain language summaries has revealed background explanation as a key strategy to increase accessibility. Such explanation is challenging for neural models to generate because it goes beyond simplification by adding content absent from the source. We derive two specialized paired corpora from CELLS to address key challenges in lay language generation: generating background explanations and simplifying the original abstract. We adopt retrieval-augmented models as an intuitive fit for the task of background explanation generation, and show improvements in summary quality and simplicity while maintaining factual correctness. Taken together, this work presents the first comprehensive study of background explanation for lay language generation, paving the path for disseminating scientific knowledge to a broader audience. CELLS is publicly available at: https://github.com/LinguisticAnomalies/pls_retrieval.

Honglin Xiong, Sheng Wang, Yitao Zhu et al.

The recent progress of large language models (LLMs), including ChatGPT and GPT-4, in comprehending and responding to human instructions has been remarkable. Nevertheless, these models typically perform better in English and have not been explicitly trained for the medical domain, resulting in suboptimal precision in diagnoses, drug recommendations, and other medical advice. Additionally, training and deploying a dialogue model is still believed to be impossible for hospitals, hindering the promotion of LLMs. To tackle these challenges, we have collected databases of medical dialogues in Chinese with ChatGPT's help and adopted several techniques to train an easy-deploy LLM. Remarkably, we were able to fine-tune the ChatGLM-6B on a single A100 80G in 13 hours, which means having a healthcare-purpose LLM can be very affordable. DoctorGLM is currently an early-stage engineering attempt and contain various mistakes. We are sharing it with the broader community to invite feedback and suggestions to improve its healthcare-focused capabilities: https://github.com/xionghonglin/DoctorGLM.

Xiangyu Zhao, Zengxin Qi, Sheng Wang et al.

Medical image segmentation methods are generally designed as fully-supervised to guarantee model performance, which require a significant amount of expert annotated samples that are high-cost and laborious. Semi-supervised image segmentation can alleviate the problem by utilizing a large number of unlabeled images along with limited labeled images. However, learning a robust representation from numerous unlabeled images remains challenging due to potential noise in pseudo labels and insufficient class separability in feature space, which undermines the performance of current semi-supervised segmentation approaches. To address the issues above, we propose a novel semi-supervised segmentation method named as Rectified Contrastive Pseudo Supervision (RCPS), which combines a rectified pseudo supervision and voxel-level contrastive learning to improve the effectiveness of semi-supervised segmentation. Particularly, we design a novel rectification strategy for the pseudo supervision method based on uncertainty estimation and consistency regularization to reduce the noise influence in pseudo labels. Furthermore, we introduce a bidirectional voxel contrastive loss to the network to ensure intra-class consistency and inter-class contrast in feature space, which increases class separability in the segmentation. The proposed RCPS segmentation method has been validated on two public datasets and an in-house clinical dataset. Experimental results reveal that the proposed method yields better segmentation performance compared with the state-of-the-art methods in semi-supervised medical image segmentation. The source code is available at https://github.com/hsiangyuzhao/RCPS.

Mehmet Saygın Seyfioğlu, Zixuan Liu, Pranav Kamath et al. · stanford

We propose a novel framework for Alzheimer's disease (AD) detection using brain MRIs. The framework starts with a data augmentation method called Brain-Aware Replacements (BAR), which leverages a standard brain parcellation to replace medically-relevant 3D brain regions in an anchor MRI from a randomly picked MRI to create synthetic samples. Ground truth "hard" labels are also linearly mixed depending on the replacement ratio in order to create "soft" labels. BAR produces a great variety of realistic-looking synthetic MRIs with higher local variability compared to other mix-based methods, such as CutMix. On top of BAR, we propose using a soft-label-capable supervised contrastive loss, aiming to learn the relative similarity of representations that reflect how mixed are the synthetic MRIs using our soft labels. This way, we do not fully exhaust the entropic capacity of our hard labels, since we only use them to create soft labels and synthetic MRIs through BAR. We show that a model pre-trained using our framework can be further fine-tuned with a cross-entropy loss using the hard labels that were used to create the synthetic samples. We validated the performance of our framework in a binary AD detection task against both from-scratch supervised training and state-of-the-art self-supervised training plus fine-tuning approaches. Then we evaluated BAR's individual performance compared to another mix-based method CutMix by integrating it within our framework. We show that our framework yields superior results in both precision and recall for the AD detection task.

Sheng Wang, Xi Ouyang, Tianming Liu et al.

When deep neural network (DNN) was first introduced to the medical image analysis community, researchers were impressed by its performance. However, it is evident now that a large number of manually labeled data is often a must to train a properly functioning DNN. This demand for supervision data and labels is a major bottleneck in current medical image analysis, since collecting a large number of annotations from experienced experts can be time-consuming and expensive. In this paper, we demonstrate that the eye movement of radiologists reading medical images can be a new form of supervision to train the DNN-based computer-aided diagnosis (CAD) system. Particularly, we record the tracks of the radiologists' gaze when they are reading images. The gaze information is processed and then used to supervise the DNN's attention via an Attention Consistency module. To the best of our knowledge, the above pipeline is among the earliest efforts to leverage expert eye movement for deep-learning-based CAD. We have conducted extensive experiments on knee X-ray images for osteoarthritis assessment. The results show that our method can achieve considerable improvement in diagnosis performance, with the help of gaze supervision.

Cai Yang, Addie Woicik, Hoifung Poon et al. · stanford

Language models pre-trained on scientific literature corpora have substantially advanced scientific discovery by offering high-quality feature representations for downstream applications. However, these features are often not interpretable, and thus can reveal limited insights to domain experts. Instead of obtaining features from language models, we propose BLIAM, a literature-based data synthesis approach to directly generate training data points that are interpretable and model-agnostic to downstream applications. The key idea of BLIAM is to create prompts using existing training data and then use these prompts to synthesize new data points. BLIAM performs these two steps iteratively as new data points will define more informative prompts and new prompts will in turn synthesize more accurate data points. Notably, literature-based data augmentation might introduce data leakage since labels of test data points in downstream applications might have already been mentioned in the language model corpus. To prevent such leakage, we introduce GDSC-combo, a large-scale drug combination discovery dataset that was published after the biomedical language model was trained. We found that BLIAM substantially outperforms a non-augmented approach and manual prompting in this rigorous data split setting. BLIAM can be further used to synthesize data points for novel drugs and cell lines that were not even measured in biomedical experiments. In addition to the promising prediction performance, the data points synthesized by BLIAM are interpretable and model-agnostic, enabling in silico augmentation for in vitro experiments.

Han Xie, Da Zheng, Jun Ma et al. · amazon-science

Model pre-training on large text corpora has been demonstrated effective for various downstream applications in the NLP domain. In the graph mining domain, a similar analogy can be drawn for pre-training graph models on large graphs in the hope of benefiting downstream graph applications, which has also been explored by several recent studies. However, no existing study has ever investigated the pre-training of text plus graph models on large heterogeneous graphs with abundant textual information (a.k.a. large graph corpora) and then fine-tuning the model on different related downstream applications with different graph schemas. To address this problem, we propose a framework of graph-aware language model pre-training (GALM) on a large graph corpus, which incorporates large language models and graph neural networks, and a variety of fine-tuning methods on downstream applications. We conduct extensive experiments on Amazon's real internal datasets and large public datasets. Comprehensive empirical results and in-depth analysis demonstrate the effectiveness of our proposed methods along with lessons learned.

Zhengliang Liu, Tianyang Zhong, Yiwei Li et al.

The rise of large language models (LLMs) has marked a pivotal shift in the field of natural language processing (NLP). LLMs have revolutionized a multitude of domains, and they have made a significant impact in the medical field. Large language models are now more abundant than ever, and many of these models exhibit bilingual capabilities, proficient in both English and Chinese. However, a comprehensive evaluation of these models remains to be conducted. This lack of assessment is especially apparent within the context of radiology NLP. This study seeks to bridge this gap by critically evaluating thirty two LLMs in interpreting radiology reports, a crucial component of radiology NLP. Specifically, the ability to derive impressions from radiologic findings is assessed. The outcomes of this evaluation provide key insights into the performance, strengths, and weaknesses of these LLMs, informing their practical applications within the medical domain.

Sheng Wang, Zihao Zhao, Xi Ouyang et al.

Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical licensing exam. However, LLMs currently have difficulty processing images, making it challenging to interpret information from medical images, which are rich in information that supports clinical decisions. On the other hand, computer-aided diagnosis (CAD) networks for medical images have seen significant success in the medical field by using advanced deep-learning algorithms to support clinical decision-making. This paper presents a method for integrating LLMs into medical-image CAD networks. The proposed framework uses LLMs to enhance the output of multiple CAD networks, such as diagnosis networks, lesion segmentation networks, and report generation networks, by summarizing and reorganizing the information presented in natural language text format. The goal is to merge the strengths of LLMs' medical domain knowledge and logical reasoning with the vision understanding capability of existing medical-image CAD models to create a more user-friendly and understandable system for patients compared to conventional CAD systems. In the future, LLM's medical knowledge can be also used to improve the performance of vision-based medical-image CAD models.

Jiyue Jiang, Pengan Chen, Liheng Chen et al. · oxford

The rapid evolution of large language models (LLMs) has transformed the competitive landscape in natural language processing (NLP), particularly for English and other data-rich languages. However, underrepresented languages like Cantonese, spoken by over 85 million people, face significant development gaps, which is particularly concerning given the economic significance of the Guangdong-Hong Kong-Macau Greater Bay Area, and in substantial Cantonese-speaking populations in places like Singapore and North America. Despite its wide use, Cantonese has scant representation in NLP research, especially compared to other languages from similarly developed regions. To bridge these gaps, we outline current Cantonese NLP methods and introduce new benchmarks designed to evaluate LLM performance in factual generation, mathematical logic, complex reasoning, and general knowledge in Cantonese, which aim to advance open-source Cantonese LLM technology. We also propose future research directions and recommended models to enhance Cantonese LLM development.

Chong Ma, Lin Zhao, Yuzhong Chen et al.

Learning harmful shortcuts such as spurious correlations and biases prevents deep neural networks from learning the meaningful and useful representations, thus jeopardizing the generalizability and interpretability of the learned representation. The situation becomes even more serious in medical imaging, where the clinical data (e.g., MR images with pathology) are limited and scarce while the reliability, generalizability and transparency of the learned model are highly required. To address this problem, we propose to infuse human experts' intelligence and domain knowledge into the training of deep neural networks. The core idea is that we infuse the visual attention information from expert radiologists to proactively guide the deep model to focus on regions with potential pathology and avoid being trapped in learning harmful shortcuts. To do so, we propose a novel eye-gaze-guided vision transformer (EG-ViT) for diagnosis with limited medical image data. We mask the input image patches that are out of the radiologists' interest and add an additional residual connection in the last encoder layer of EG-ViT to maintain the correlations of all patches. The experiments on two public datasets of INbreast and SIIM-ACR demonstrate our EG-ViT model can effectively learn/transfer experts' domain knowledge and achieve much better performance than baselines. Meanwhile, it successfully rectifies the harmful shortcut learning and significantly improves the EG-ViT model's interpretability. In general, EG-ViT takes the advantages of both human expert's prior knowledge and the power of deep neural networks. This work opens new avenues for advancing current artificial intelligence paradigms by infusing human intelligence.

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.

Fenglin Liu, Bang Yang, Chenyu You et al. · oxford

Gene Ontology (GO) is the primary gene function knowledge base that enables computational tasks in biomedicine. The basic element of GO is a term, which includes a set of genes with the same function. Existing research efforts of GO mainly focus on predicting gene term associations. Other tasks, such as generating descriptions of new terms, are rarely pursued. In this paper, we propose a novel task: GO term description generation. This task aims to automatically generate a sentence that describes the function of a GO term belonging to one of the three categories, i.e., molecular function, biological process, and cellular component. To address this task, we propose a Graph-in-Graph network that can efficiently leverage the structural information of GO. The proposed network introduces a two-layer graph: the first layer is a graph of GO terms where each node is also a graph (gene graph). Such a Graph-in-Graph network can derive the biological functions of GO terms and generate proper descriptions. To validate the effectiveness of the proposed network, we build three large-scale benchmark datasets. By incorporating the proposed Graph-in-Graph network, the performances of seven different sequence-to-sequence models can be substantially boosted across all evaluation metrics, with up to 34.7%, 14.5%, and 39.1% relative improvements in BLEU, ROUGE-L, and METEOR, respectively.

Lu Yang, Sheng Wang, Russ B. Altman

Objective For the UK Biobank standardized phenotype codes are associated with patients who have been hospitalized but are missing for many patients who have been treated exclusively in an outpatient setting. We describe a method for phenotype recognition that imputes phenotype codes for all UK Biobank participants. Materials and Methods POPDx (Population-based Objective Phenotyping by Deep Extrapolation) is a bilinear machine learning framework for simultaneously estimating the probabilities of 1,538 phenotype codes. We extracted phenotypic and health-related information of 392,246 individuals from the UK Biobank for POPDx development and evaluation. A total of 12,803 ICD-10 diagnosis codes of the patients were converted to 1,538 Phecodes as gold standard labels. The POPDx framework was evaluated and compared to other available methods on automated multi-phenotype recognition. Results POPDx can predict phenotypes that are rare or even unobserved in training. We demonstrate substantial improvement of automated multi-phenotype recognition across 22 disease categories, and its application in identifying key epidemiological features associated with each phenotype. Conclusions POPDx helps provide well-defined cohorts for downstream studies. It is a general purpose method that can be applied to other biobanks with diverse but incomplete data.

Tao Shen, Zhihang Hu, Siqi Sun et al.

Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design. The structural flexibility of RNA, which leads to scarcity of experimentally determined data, complicates computational prediction efforts. Here, we present RhoFold+, an RNA language model-based deep learning method that accurately predicts 3D structures of single-chain RNAs from sequences. By integrating an RNA language model pre-trained on ~23.7 million RNA sequences and leveraging techniques to address data scarcity, RhoFold+ offers a fully automated end-to-end pipeline for RNA 3D structure prediction. Retrospective evaluations on RNA-Puzzles and CASP15 natural RNA targets demonstrate RhoFold+'s superiority over existing methods, including human expert groups. Its efficacy and generalizability are further validated through cross-family and cross-type assessments, as well as time-censored benchmarks. Additionally, RhoFold+ predicts RNA secondary structures and inter-helical angles, providing empirically verifiable features that broaden its applicability to RNA structure and function studies.

Jiaqi Liu, Shi Qiu, Mairui Li et al.

Automating scientific discovery requires more than generating papers from ideas. Real research is iterative: hypotheses are challenged from multiple perspectives, experiments fail and inform the next attempt, and lessons accumulate across cycles. Existing autonomous research systems often model this process as a linear pipeline: they rely on single-agent reasoning, stop when execution fails, and do not carry experience across runs. We present AutoResearchClaw, a multi-agent autonomous research pipeline built on five mechanisms: structured multi-agent debate for hypothesis generation and result analysis, a self-healing executor with a \textsc{Pivot}/\textsc{Refine} decision loop that transforms failures into information, verifiable result reporting that prevents fabricated numbers and hallucinated citations, human-in-the-loop collaboration with seven intervention modes spanning full autonomy to step-by-step oversight, and cross-run evolution that converts past mistakes into future safeguards. On ARC-Bench, a 25-topic experiment-stage benchmark, AutoResearchClaw outperforms AI Scientist v2 by 54.7%. A human-in-the-loop ablation across seven intervention modes reveals that precise, targeted collaboration at high-leverage decision points consistently outperforms both full autonomy and exhaustive step-by-step oversight. We position AutoResearchClaw as a research amplifier that augments rather than replaces human scientific judgment. Code is available at https://github.com/aiming-lab/AutoResearchClaw.

Jinxin Lv, Xiaoyu Zeng, Sheng Wang et al.

One-shot segmentation of brain tissues is typically a dual-model iterative learning: a registration model (reg-model) warps a carefully-labeled atlas onto unlabeled images to initialize their pseudo masks for training a segmentation model (seg-model); the seg-model revises the pseudo masks to enhance the reg-model for a better warping in the next iteration. However, there is a key weakness in such dual-model iteration that the spatial misalignment inevitably caused by the reg-model could misguide the seg-model, which makes it converge on an inferior segmentation performance eventually. In this paper, we propose a novel image-aligned style transformation to reinforce the dual-model iterative learning for robust one-shot segmentation of brain tissues. Specifically, we first utilize the reg-model to warp the atlas onto an unlabeled image, and then employ the Fourier-based amplitude exchange with perturbation to transplant the style of the unlabeled image into the aligned atlas. This allows the subsequent seg-model to learn on the aligned and style-transferred copies of the atlas instead of unlabeled images, which naturally guarantees the correct spatial correspondence of an image-mask training pair, without sacrificing the diversity of intensity patterns carried by the unlabeled images. Furthermore, we introduce a feature-aware content consistency in addition to the image-level similarity to constrain the reg-model for a promising initialization, which avoids the collapse of image-aligned style transformation in the first iteration. Experimental results on two public datasets demonstrate 1) a competitive segmentation performance of our method compared to the fully-supervised method, and 2) a superior performance over other state-of-the-art with an increase of average Dice by up to 4.67%. The source code is available at: https://github.com/JinxLv/One-shot-segmentation-via-IST.

Yu Zhang, Yu Meng, Xuan Wang et al.

Discovering latent topics from text corpora has been studied for decades. Many existing topic models adopt a fully unsupervised setting, and their discovered topics may not cater to users' particular interests due to their inability of leveraging user guidance. Although there exist seed-guided topic discovery approaches that leverage user-provided seeds to discover topic-representative terms, they are less concerned with two factors: (1) the existence of out-of-vocabulary seeds and (2) the power of pre-trained language models (PLMs). In this paper, we generalize the task of seed-guided topic discovery to allow out-of-vocabulary seeds. We propose a novel framework, named SeeTopic, wherein the general knowledge of PLMs and the local semantics learned from the input corpus can mutually benefit each other. Experiments on three real datasets from different domains demonstrate the effectiveness of SeeTopic in terms of topic coherence, accuracy, and diversity.

Sheng Wang, Eric Johnsen

We consider implementations of high-order finite difference Weighted Essentially Non-Oscillatory (WENO) schemes for the Euler equations in cylindrical and spherical coordinate systems with radial dependence only. The main concern of this work lies in ensuring both high-order accuracy and conservation. Three different spatial discretizations are assessed: one that is shown to be high-order accurate but not conservative, one conservative but not high-order accurate, and a new approach that is both high-order accurate and conservative. For cylindrical and spherical coordinates, we present convergence results for the advection equation and the Euler equations with an acoustics problem; we then use the Sod shock tube and the Sedov point-blast problems in cylindrical coordinates to verify our analysis and implementations.

Yitao Zhu, Zhenrong Shen, Zihao Zhao et al.

The common practice in developing computer-aided diagnosis (CAD) models based on transformer architectures usually involves fine-tuning from ImageNet pre-trained weights. However, with recent advances in large-scale pre-training and the practice of scaling laws, Vision Transformers (ViT) have become much larger and less accessible to medical imaging communities. Additionally, in real-world scenarios, the deployments of multiple CAD models can be troublesome due to problems such as limited storage space and time-consuming model switching. To address these challenges, we propose a new method MeLo (Medical image Low-rank adaptation), which enables the development of a single CAD model for multiple clinical tasks in a lightweight manner. It adopts low-rank adaptation instead of resource-demanding fine-tuning. By fixing the weight of ViT models and only adding small low-rank plug-ins, we achieve competitive results on various diagnosis tasks across different imaging modalities using only a few trainable parameters. Specifically, our proposed method achieves comparable performance to fully fine-tuned ViT models on four distinct medical imaging datasets using about 0.17% trainable parameters. Moreover, MeLo adds only about 0.5MB of storage space and allows for extremely fast model switching in deployment and inference. Our source code and pre-trained weights are available on our website (https://absterzhu.github.io/melo.github.io/).

Kyrie Zhao, Zehong Wang, Tianyi Ma et al.

Hypergraphs model higher-order relations that drive real-world decisions, from drug prescriptions to recommendations. A central structural signal in such data, beyond what pairwise relations can express, is interaction compositionality: whether a higher-order relation is compositional, emergent, or inhibitory with respect to its observed or unobserved sets. In polypharmacy, the regime decides whether a drug should be dropped, kept, or excluded: a compositional drug triple can be safely simplified, an emergent triple requires all drugs jointly, and an inhibitory triple flags a drug that disrupts an existing interaction. However, existing hypergraph learning methods, which merely propagate messages over observed hyperedges, leave this compositional signal unmodeled, allowing dangerous drug combinations to slip through and be misclassified. To this end, we propose the Hypergraph Pattern Machine (HGPM), shifting the paradigm from message passing to learning the compositional pattern of subsets. It tokenizes compositional subsets, organizes them in an inclusion DAG, and trains an inclusion-aware Transformer under masked reconstruction. On ten hypergraph benchmarks, HGPM matches or exceeds state-of-the-art methods. Notably, in a real adverse-event prediction case, HGPM correctly identifies the drug addition that inhibits the side effect among feature-identical candidates, a discrimination existing methods cannot make. The code and data are in https://github.com/KryieZhao/HGPM.git.

Yuezhang Peng, Chonghao Cai, Ziang Liu et al.

Spoken Language Understanding (SLU), which aims to extract user semantics to execute downstream tasks, is a crucial component of task-oriented dialog systems. Existing SLU datasets generally lack sufficient diversity and complexity, and there is an absence of a unified benchmark for the latest Large Language Models (LLMs) and Large Audio Language Models (LALMs). This work introduces MAC-SLU, a novel Multi-Intent Automotive Cabin Spoken Language Understanding Dataset, which increases the difficulty of the SLU task by incorporating authentic and complex multi-intent data. Based on MAC-SLU, we conducted a comprehensive benchmark of leading open-source LLMs and LALMs, covering methods like in-context learning, supervised fine-tuning (SFT), and end-to-end (E2E) and pipeline paradigms. Our experiments show that while LLMs and LALMs have the potential to complete SLU tasks through in-context learning, their performance still lags significantly behind SFT. Meanwhile, E2E LALMs demonstrate performance comparable to pipeline approaches and effectively avoid error propagation from speech recognition. Code\footnote{https://github.com/Gatsby-web/MAC\_SLU} and datasets\footnote{huggingface.co/datasets/Gatsby1984/MAC\_SLU} are released publicly.

Zhenrong Shen, Maosong Cao, Sheng Wang et al.

Automatic examination of thin-prep cytologic test (TCT) slides can assist pathologists in finding cervical abnormality for accurate and efficient cancer screening. Current solutions mostly need to localize suspicious cells and classify abnormality based on local patches, concerning the fact that whole slide images of TCT are extremely large. It thus requires many annotations of normal and abnormal cervical cells, to supervise the training of the patch-level classifier for promising performance. In this paper, we propose CellGAN to synthesize cytopathological images of various cervical cell types for augmenting patch-level cell classification. Built upon a lightweight backbone, CellGAN is equipped with a non-linear class mapping network to effectively incorporate cell type information into image generation. We also propose the Skip-layer Global Context module to model the complex spatial relationship of the cells, and attain high fidelity of the synthesized images through adversarial learning. Our experiments demonstrate that CellGAN can produce visually plausible TCT cytopathological images for different cell types. We also validate the effectiveness of using CellGAN to greatly augment patch-level cell classification performance.

Zehong Wang, Xiaolong Han, Qi Yang et al.

Molecular representations fundamentally shape how machine learning systems reason about molecular structure and physical properties. Most existing approaches adopt a discrete pipeline: molecules are encoded as sequences, graphs, or point clouds, mapped to fixed-dimensional embeddings, and then used for task-specific prediction. This paradigm treats molecules as discrete objects, despite their intrinsically continuous and field-like physical nature. We argue that molecular learning can instead be formulated as learning in function space. Specifically, we model each molecule as a continuous function over three-dimensional (3D) space and treat this molecular field as the primary object of representation. From this perspective, conventional molecular representations arise as particular sampling schemes of an underlying continuous object. We instantiate this formulation with MolField, a hyper-network-based framework that learns distributions over molecular fields. To ensure physical consistency, these functions are defined over canonicalized coordinates, yielding invariance to global SE(3) transformations. To enable learning directly over functions, we introduce a structured weight tokenization and train a sequence-based hyper-network to model a shared prior over molecular fields. We evaluate MolField on molecular dynamics and property prediction. Our results show that treating molecules as continuous functions fundamentally changes how molecular representations generalize across tasks and yields downstream behavior that is stable to how molecules are discretized or queried.

Xin Wang, Sheng Wang, Honglin Xiong et al.

Magnetic resonance (MR) images collected in 2D clinical protocols typically have large inter-slice spacing, resulting in high in-plane resolution and reduced through-plane resolution. Super-resolution technique can enhance the through-plane resolution of MR images to facilitate downstream visualization and computer-aided diagnosis. However, most existing works train the super-resolution network at a fixed scaling factor, which is not friendly to clinical scenes of varying inter-slice spacing in MR scanning. Inspired by the recent progress in implicit neural representation, we propose a Spatial Attention-based Implicit Neural Representation (SA-INR) network for arbitrary reduction of MR inter-slice spacing. The SA-INR aims to represent an MR image as a continuous implicit function of 3D coordinates. In this way, the SA-INR can reconstruct the MR image with arbitrary inter-slice spacing by continuously sampling the coordinates in 3D space. In particular, a local-aware spatial attention operation is introduced to model nearby voxels and their affinity more accurately in a larger receptive field. Meanwhile, to improve the computational efficiency, a gradient-guided gating mask is proposed for applying the local-aware spatial attention to selected areas only. We evaluate our method on the public HCP-1200 dataset and the clinical knee MR dataset to demonstrate its superiority over other existing methods.

Zixuan Liu, Gaurush Hiranandani, Kun Qian et al.

Developing text mining approaches to mine aspects from customer reviews has been well-studied due to its importance in understanding customer needs and product attributes. In contrast, it remains unclear how to predict the future emerging aspects of a new product that currently has little review information. This task, which we named product aspect forecasting, is critical for recommending new products, but also challenging because of the missing reviews. Here, we propose ForeSeer, a novel textual mining and product embedding approach progressively trained on temporal product graphs for this novel product aspect forecasting task. ForeSeer transfers reviews from similar products on a large product graph and exploits these reviews to predict aspects that might emerge in future reviews. A key novelty of our method is to jointly provide review, product, and aspect embeddings that are both time-sensitive and less affected by extremely imbalanced aspect frequencies. We evaluated ForeSeer on a real-world product review system containing 11,536,382 reviews and 11,000 products over 3 years. We observe that ForeSeer substantially outperformed existing approaches with at least 49.1\% AUPRC improvement under the real setting where aspect associations are not given. ForeSeer further improves future link prediction on the product graph and the review aspect association prediction. Collectively, Foreseer offers a novel framework for review forecasting by effectively integrating review text, product network, and temporal information, opening up new avenues for online shopping recommendation and e-commerce applications.

Pengchao Feng, Yao Xiao, Ziyang Ma et al.

Recent advances in text-to-speech (TTS) have yielded remarkable improvements in naturalness and intelligibility. Building on these achievements, research has increasingly shifted toward enhancing the expressiveness of generated speech, such as dialectal and emotional TTS. However, cross-style synthesis combining both dialect and emotion remains challenging and largely unexplored, mainly due to the scarcity of dialectal data with emotional labels. To address this, we propose Hierarchical Expressive Vector (HE-Vector), a two-stage method for Emotional Dialectal TTS. In the first stage, we construct different task vectors to model dialectal and emotional styles independently, and then enhance single-style synthesis by adjusting their weights, a method we refer to as Expressive Vector (E-Vector). For the second stage, we hierarchically integrate these vectors to achieve controllable emotionally expressive dialect synthesis without requiring jointly labeled data, corresponding to Hierarchical Expressive Vector (HE-Vector). Experimental results demonstrate that HE-Vectors achieve superior performance in dialect synthesis, and promising results in synthesizing emotionally expressive dialectal speech in a zero-shot setting.

Xin Wang, Zhenrong Shen, Zhiyun Song et al.

Magnetic resonance (MR) images collected in 2D scanning protocols typically have large inter-slice spacing, resulting in high in-plane resolution but reduced through-plane resolution. Super-resolution techniques can reduce the inter-slice spacing of 2D scanned MR images, facilitating the downstream visual experience and computer-aided diagnosis. However, most existing super-resolution methods are trained at a fixed scaling ratio, which is inconvenient in clinical settings where MR scanning may have varying inter-slice spacings. To solve this issue, we propose Hierarchical Feature Conditional Diffusion (HiFi-Diff)} for arbitrary reduction of MR inter-slice spacing. Given two adjacent MR slices and the relative positional offset, HiFi-Diff can iteratively convert a Gaussian noise map into any desired in-between MR slice. Furthermore, to enable fine-grained conditioning, the Hierarchical Feature Extraction (HiFE) module is proposed to hierarchically extract conditional features and conduct element-wise modulation. Our experimental results on the publicly available HCP-1200 dataset demonstrate the high-fidelity super-resolution capability of HiFi-Diff and its efficacy in enhancing downstream segmentation performance.

Zhiyun Song, Zengxin Qi, Xin Wang et al.

Cross-modality synthesis (CMS), super-resolution (SR), and their combination (CMSR) have been extensively studied for magnetic resonance imaging (MRI). Their primary goals are to enhance the imaging quality by synthesizing the desired modality and reducing the slice thickness. Despite the promising synthetic results, these techniques are often tailored to specific tasks, thereby limiting their adaptability to complex clinical scenarios. Therefore, it is crucial to build a unified network that can handle various image synthesis tasks with arbitrary requirements of modality and resolution settings, so that the resources for training and deploying the models can be greatly reduced. However, none of the previous works is capable of performing CMS, SR, and CMSR using a unified network. Moreover, these MRI reconstruction methods often treat alias frequencies improperly, resulting in suboptimal detail restoration. In this paper, we propose a Unified Co-Modulated Alias-free framework (Uni-COAL) to accomplish the aforementioned tasks with a single network. The co-modulation design of the image-conditioned and stochastic attribute representations ensures the consistency between CMS and SR, while simultaneously accommodating arbitrary combinations of input/output modalities and thickness. The generator of Uni-COAL is also designed to be alias-free based on the Shannon-Nyquist signal processing framework, ensuring effective suppression of alias frequencies. Additionally, we leverage the semantic prior of Segment Anything Model (SAM) to guide Uni-COAL, ensuring a more authentic preservation of anatomical structures during synthesis. Experiments on three datasets demonstrate that Uni-COAL outperforms the alternatives in CMS, SR, and CMSR tasks for MR images, which highlights its generalizability to wide-range applications.

Zheren Li, Zhiming Cui, Lichi Zhang et al.

The deep learning technique has been shown to be effectively addressed several image analysis tasks in the computer-aided diagnosis scheme for mammography. The training of an efficacious deep learning model requires large data with diverse styles and qualities. The diversity of data often comes from the use of various scanners of vendors. But, in practice, it is impractical to collect a sufficient amount of diverse data for training. To this end, a novel contrastive learning is developed to equip the deep learning models with better style generalization capability. Specifically, the multi-style and multi-view unsupervised self-learning scheme is carried out to seek robust feature embedding against style diversity as a pretrained model. Afterward, the pretrained network is further fine-tuned to the downstream tasks, e.g., mass detection, matching, BI-RADS rating, and breast density classification. The proposed method has been evaluated extensively and rigorously with mammograms from various vendor style domains and several public datasets. The experimental results suggest that the proposed domain generalization method can effectively improve performance of four mammographic image tasks on the data from both seen and unseen domains, and outperform many state-of-the-art (SOTA) generalization methods.

Xiangyu Zhao, Di Zang, Sheng Wang et al.

Brain network analysis for traumatic brain injury (TBI) patients is critical for its consciousness level assessment and prognosis evaluation, which requires the segmentation of certain consciousness-related brain regions. However, it is difficult to construct a TBI segmentation model as manually annotated MR scans of TBI patients are hard to collect. Data augmentation techniques can be applied to alleviate the issue of data scarcity. However, conventional data augmentation strategies such as spatial and intensity transformation are unable to mimic the deformation and lesions in traumatic brains, which limits the performance of the subsequent segmentation task. To address these issues, we propose a novel medical image inpainting model named TBI-GAN to synthesize TBI MR scans with paired brain label maps. The main strength of our TBI-GAN method is that it can generate TBI images and corresponding label maps simultaneously, which has not been achieved in the previous inpainting methods for medical images. We first generate the inpainted image under the guidance of edge information following a coarse-to-fine manner, and then the synthesized intensity image is used as the prior for label inpainting. Furthermore, we introduce a registration-based template augmentation pipeline to increase the diversity of the synthesized image pairs and enhance the capacity of data augmentation. Experimental results show that the proposed TBI-GAN method can produce sufficient synthesized TBI images with high quality and valid label maps, which can greatly improve the 2D and 3D traumatic brain segmentation performance compared with the alternatives.

Peng Xia, Kangyu Zhu, Haoran Li et al.

Artificial Intelligence (AI) has demonstrated significant potential in healthcare, particularly in disease diagnosis and treatment planning. Recent progress in Medical Large Vision-Language Models (Med-LVLMs) has opened up new possibilities for interactive diagnostic tools. However, these models often suffer from factual hallucination, which can lead to incorrect diagnoses. Fine-tuning and retrieval-augmented generation (RAG) have emerged as methods to address these issues. However, the amount of high-quality data and distribution shifts between training data and deployment data limit the application of fine-tuning methods. Although RAG is lightweight and effective, existing RAG-based approaches are not sufficiently general to different medical domains and can potentially cause misalignment issues, both between modalities and between the model and the ground truth. In this paper, we propose a versatile multimodal RAG system, MMed-RAG, designed to enhance the factuality of Med-LVLMs. Our approach introduces a domain-aware retrieval mechanism, an adaptive retrieved contexts selection method, and a provable RAG-based preference fine-tuning strategy. These innovations make the RAG process sufficiently general and reliable, significantly improving alignment when introducing retrieved contexts. Experimental results across five medical datasets (involving radiology, ophthalmology, pathology) on medical VQA and report generation demonstrate that MMed-RAG can achieve an average improvement of 43.8% in the factual accuracy of Med-LVLMs. Our data and code are available in https://github.com/richard-peng-xia/MMed-RAG.

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.

Juncheng Hu, Ziteng Xue, Guotao Liang et al.

We introduce AmodalSVG, a new framework for amodal image vectorization that produces semantically organized and geometrically complete SVG representations from natural images. Existing vectorization methods operate under a modal paradigm: tracing only visible pixels and disregarding occlusion. Consequently, the resulting SVGs are semantically entangled and geometrically incomplete, limiting SVG's structural editability. In contrast, AmodalSVG reconstructs full object geometries, including occluded regions, into independent, editable vector layers. To achieve this, AmodalSVG reformulates image vectorization as a two-stage framework, performing semantic decoupling and completion in the raster domain to produce amodally complete semantic layers, which are then independently vectorized. In the first stage, we introduce Semantic Layer Peeling (SLP), a VLM-guided strategy that progressively decomposes an image into semantically coherent layers. By hybrid inpainting, SLP recovers complete object appearances under occlusions, enabling explicit semantic decoupling. To vectorize these layers efficiently, we propose Adaptive Layered Vectorization (ALV), which dynamically modulates the primitive budget via an error-budget-driven adjustment mechanism. Extensive experiments demonstrate that AmodalSVG significantly outperforms prior methods in visual fidelity. Moreover, the resulting amodal layers enable object-level editing directly in the vector domain, capabilities not supported by existing vectorization approaches. Code will be released upon acceptance.

Xu Liu, Yongheng Zhang, Qiguang Chen et al.

Recently, Interleaved-modal Chain-of-Thought (ICoT) reasoning has achieved remarkable success by leveraging both multimodal inputs and outputs, attracting increasing attention. While achieving promising performance, current ICoT methods still suffer from two major limitations: (1) Static Visual Thought Positioning, which statically inserts visual information at fixed steps, resulting in inefficient and inflexible reasoning; and (2) Broken Visual Thought Representation, which involves discontinuous and semantically incoherent visual tokens. To address these limitations, we introduce Interleaved-modal Chain-of-Thought reasoning with Dynamic and Precise Visual Thoughts (DaP-ICoT), which incorporates two key components: (1) Dynamic Visual Thought Integration adaptively introduces visual inputs based on reasoning needs, reducing redundancy and improving efficiency. (2) Precise Visual Thought Guidance ensures visual semantically coherent and contextually aligned representations. Experiments across multiple benchmarks and models demonstrate that DaP-ICoT achieves state-of-the-art performance. In addition, DaP-ICoT significantly reduces the number of inserted images, leading to a 72.6% decrease in token consumption, enabling more efficient ICoT reasoning.

Fangrui Huang, Souhad Chbeir, Arpandeep Khatua et al.

Large language models (LLMs) are increasingly used for mental-health support; yet prevailing evaluation methods--fluency metrics, preference tests, and generic dialogue benchmarks--fail to capture the clinically critical dimensions of psychotherapy. We introduce THERAPYGYM, a framework that evaluates and improves therapy chatbots along two clinical pillars: fidelity and safety. Fidelity is measured using the Cognitive Therapy Rating Scale (CTRS), implemented as an automated pipeline that scores adherence to CBT techniques over multi-turn sessions. Safety is assessed using a multi-label annotation scheme, covering therapy-specific risks (e.g., failing to address harm or abuse). To mitigate bias and unreliability in LLM-based judges, we further release THERAPYJUDGEBENCH, a validation set of 116 dialogues with 1,270 expert ratings for auditing and calibration against licensed clinicians. THERAPYGYM also serves as a training harness: CTRS and safety-based rewards drive RL with configurable patient simulations spanning diverse symptom profiles. Models trained in THERAPYGYM improve on expert ratings, with average CTRS rising from 0.10 to 0.60 (and 0.16 to 0.59 under LLM judges). Our work enables scalable development of therapy chatbots that are faithful to evidence-based practice and safer in high-stakes use.

Zihao Zhao, Yuxiao Liu, Han Wu et al.

Contrastive Language-Image Pre-training (CLIP), a simple yet effective pre-training paradigm, successfully introduces text supervision to vision models. It has shown promising results across various tasks due to its generalizability and interpretability. The use of CLIP has recently gained increasing interest in the medical imaging domain, serving as a pre-training paradigm for image-text alignment, or a critical component in diverse clinical tasks. With the aim of facilitating a deeper understanding of this promising direction, this survey offers an in-depth exploration of the CLIP within the domain of medical imaging, regarding both refined CLIP pre-training and CLIP-driven applications. In this paper, we (1) first start with a brief introduction to the fundamentals of CLIP methodology; (2) then investigate the adaptation of CLIP pre-training in the medical imaging domain, focusing on how to optimize CLIP given characteristics of medical images and reports; (3) further explore practical utilization of CLIP pre-trained models in various tasks, including classification, dense prediction, and cross-modal tasks; and (4) finally discuss existing limitations of CLIP in the context of medical imaging, and propose forward-looking directions to address the demands of medical imaging domain. Studies featuring technical and practical value are both investigated. We expect this survey will provide researchers with a holistic understanding of the CLIP paradigm and its potential implications. The project page of this survey can also be found on https://github.com/zhaozh10/Awesome-CLIP-in-Medical-Imaging.

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.

Juntao Zhao, Wenhao Lu, Sheng Wang et al.

Quantization is widely adopted to accelerate inference and reduce memory consumption in large language models (LLMs). While activation-weight joint quantization enables efficient low-precision decoding, it suffers from substantial performance degradation on multi-step reasoning tasks. We propose QSpec, a novel quantization paradigm that decouples efficiency from quality by integrating two complementary schemes via speculative decoding: low-precision joint quantization for fast drafting and high-precision weight-only quantization for accurate verification. QSpec reuses both weights and KV cache across stages, enabling near-zero-cost switching without retraining or auxiliary models. Compared to high-precision baselines, QSpec achieves up to 1.64x speedup without quality degradation, and outperforms state-of-the-art speculative decoding methods by up to 1.55x in batched settings. Furthermore, QSpec supports plug-and-play deployment and generalizes well across model scales, quantization methods, and workloads. These properties make QSpec a practical and scalable solution for high-fidelity quantized LLM serving under memory-constrained scenarios. Our code is available at https://github.com/hku-netexplo-lab/QSpec.

Kangyu Zhu, Peng Xia, Yun Li et al.

The advancement of Large Vision-Language Models (LVLMs) has propelled their application in the medical field. However, Medical LVLMs (Med-LVLMs) encounter factuality challenges due to modality misalignment, where the models prioritize textual knowledge over visual input, leading to hallucinations that contradict information in medical images. Previous attempts to enhance modality alignment in Med-LVLMs through preference optimization have inadequately mitigated clinical relevance in preference data, making these samples easily distinguishable and reducing alignment effectiveness. To address this challenge, we propose MMedPO, a novel multimodal medical preference optimization approach that considers the clinical relevance of preference samples to enhance Med-LVLM alignment. MMedPO curates multimodal preference data by introducing two types of dispreference: (1) plausible hallucinations injected through target Med-LVLMs or GPT-4o to produce medically inaccurate responses, and (2) lesion region neglect achieved through local lesion-noising, disrupting visual understanding of critical areas. We then calculate clinical relevance for each sample based on scores from multiple Med-LLMs and visual tools, and integrate these scores into the preference optimization process as weights, enabling effective alignment. Our experiments demonstrate that MMedPO significantly enhances factual accuracy in Med-LVLMs, achieving substantial improvements over existing preference optimization methods by averaging 14.2% and 51.7% across the Med-VQA and report generation tasks. Our code are available in https://github.com/aiming-lab/MMedPO.

Hongbin Lin, Yiming Yang, Yifan Zhang et al.

In autonomous driving, end-to-end planners learn scene representations from raw sensor data and utilize them to generate a motion plan or control actions. However, exclusive reliance on the current scene for motion planning may result in suboptimal responses in highly dynamic traffic environments where ego actions further alter the future scene. To model the evolution of future scenes, we leverage the World Model to represent how the ego vehicle and its environment interact and change over time, which entails complex reasoning. The Chain of Thought (CoT) offers a promising solution by forecasting a sequence of future thoughts that subsequently guide trajectory refinement. In this paper, we propose FutureX, a CoT-driven pipeline that enhances end-to-end planners to perform complex motion planning via future scene latent reasoning and trajectory refinement. Specifically, the Auto-think Switch examines the current scene and decides whether additional reasoning is required to yield a higher-quality motion plan. Once FutureX enters the Thinking mode, the Latent World Model conducts a CoT-guided rollout to predict future scene representation, enabling the Summarizer Module to further refine the motion plan. Otherwise, FutureX operates in an Instant mode to generate motion plans in a forward pass for relatively simple scenes. Extensive experiments demonstrate that FutureX enhances existing methods by producing more rational motion plans and fewer collisions without compromising efficiency, thereby achieving substantial overall performance gains, e.g., 6.2 PDMS improvement for TransFuser on NAVSIM. Code will be released.

Jiahan Li, Tong Chen, Shitong Luo et al.

Peptides, short chains of amino acids, interact with target proteins, making them a unique class of protein-based therapeutics for treating human diseases. Recently, deep generative models have shown great promise in peptide generation. However, several challenges remain in designing effective peptide binders. First, not all residues contribute equally to peptide-target interactions. Second, the generated peptides must adopt valid geometries due to the constraints of peptide bonds. Third, realistic tasks for peptide drug development are still lacking. To address these challenges, we introduce PepHAR, a hot-spot-driven autoregressive generative model for designing peptides targeting specific proteins. Building on the observation that certain hot spot residues have higher interaction potentials, we first use an energy-based density model to fit and sample these key residues. Next, to ensure proper peptide geometry, we autoregressively extend peptide fragments by estimating dihedral angles between residue frames. Finally, we apply an optimization process to iteratively refine fragment assembly, ensuring correct peptide structures. By combining hot spot sampling with fragment-based extension, our approach enables de novo peptide design tailored to a target protein and allows the incorporation of key hot spot residues into peptide scaffolds. Extensive experiments, including peptide design and peptide scaffold generation, demonstrate the strong potential of PepHAR in computational peptide binder design. Source code will be available at https://github.com/Ced3-han/PepHAR.

Lin Li, Haoran Feng, Zehuan Huang et al.

We introduce SegviGen, a framework that repurposes native 3D generative models for 3D part segmentation. Existing pipelines either lift strong 2D priors into 3D via distillation or multi-view mask aggregation, often suffering from cross-view inconsistency and blurred boundaries, or explore native 3D discriminative segmentation, which typically requires large-scale annotated 3D data and substantial training resources. In contrast, SegviGen leverages the structured priors encoded in pretrained 3D generative model to induce segmentation through distinctive part colorization, establishing a novel and efficient framework for part segmentation. Specifically, SegviGen encodes a 3D asset and predicts part-indicative colors on active voxels of a geometry-aligned reconstruction. It supports interactive part segmentation, full segmentation, and full segmentation with 2D guidance in a unified framework. Extensive experiments show that SegviGen improves over the prior state of the art by 40% on interactive part segmentation and by 15% on full segmentation, while using only 0.32% of the labeled training data. It demonstrates that pretrained 3D generative priors transfer effectively to 3D part segmentation, enabling strong performance with limited supervision. See our project page at https://fenghora.github.io/SegviGen-Page/.

Jiaming Li, Junlei Wu, Sheng Wang et al.

Widespread clinical deployment of computer-aided diagnosis (CAD) systems is hindered by the challenge of integrating with existing hospital IT infrastructure. Here, we introduce VisionCAD, a vision-based radiological assistance framework that circumvents this barrier by capturing medical images directly from displays using a camera system. The framework operates through an automated pipeline that detects, restores, and analyzes on-screen medical images, transforming camera-captured visual data into diagnostic-quality images suitable for automated analysis and report generation. We validated VisionCAD across diverse medical imaging datasets, demonstrating that our modular architecture can flexibly utilize state-of-the-art diagnostic models for specific tasks. The system achieves diagnostic performance comparable to conventional CAD systems operating on original digital images, with an F1-score degradation typically less than 2\% across classification tasks, while natural language generation metrics for automated reports remain within 1\% of those derived from original images. By requiring only a camera device and standard computing resources, VisionCAD offers an accessible approach for AI-assisted diagnosis, enabling the deployment of diagnostic capabilities in diverse clinical settings without modifications to existing infrastructure.

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.

Zepeng Liu, Sheng Wang, Shixun Huang et al.

Graph-centric cross-model data integration and analytics (GCDIA) refer to tasks that leverage the graph model as a central paradigm to integrate relevant information across heterogeneous data models, such as relational and document, and subsequently perform complex analytics such as regression and similarity computation. As modern applications generate increasingly diverse data and move beyond simple retrieval toward advanced analytical objectives (e.g., prediction and recommendation), GCDIA has become increasingly important. Existing multi-model databases (MMDBs) struggle to efficiently support both integration (GCDI) and analytics (GCDA) in GCDIA. They typically separate graph processing from other models without global optimization for GCDI, while relying on tuple-at-a-time execution for GCDA, leading to limited performance and scalability. To address these limitations, we propose GredoDB, a unified MMDB that natively supports storing graph, relational, and document models, while efficiently processing GCDIA. Specifically, we design 1) topology- and attribute-aware graph operators for efficient predicate-aware traversal, 2) a unified GCDI optimization framework to exploit cross-model correlations, and 3) a parallel GCDA architecture that materializes intermediate results for operator-level execution. Experiments on the widely adopted multi-model benchmark M2Bench demonstrate that, in terms of response time, GredoDB achieves up to 107.89 times and an average of 10.89 times speedup on GCDI, and up to 356.72 times and an average of 37.79 times on GCDA, compared to state-of-the-art (SOTA) MMDBs.

Jingqi Zhou, Sheng Wang, Jingwei Dong et al.

Large vision-language models (LVLMs) have witnessed significant progress on visual understanding tasks. However, they often prioritize language knowledge over image information on visual reasoning tasks, incurring performance degradation. To tackle this issue, we first identify the drawbacks of existing solutions (i.e., limited multi-modal reasoning capacities, and insufficient and irrelevant visual descriptions). We then decompose visual reasoning process into two stages: proactive visual perception (i.e., eyesight) and textual reasoning (i.e., wisdom), and introduce a novel visual reasoning framework named ProReason. This framework features decoupled vision-reasoning capabilities and multi-run proactive perception. Briefly, given a multi-modal question, ProReason iterates proactive information collection and reasoning until the answer can be concluded with necessary and sufficient visual descriptions. Notably, the disassociation of capabilities allows seamless integration of existing large language models (LLMs) to compensate for the reasoning deficits of LVLMs. Our extensive experiments demonstrate that ProReason outperforms existing multi-step reasoning frameworks on various benchmarks for both open-source and closed-source models, with the average performance gain reaching 13.2%. Besides, the integration of LLMs allows ProReason to produce high-quality visual reasoning data, which empowers ProReason-distilled models (i.e., ProReason-VL and ProReason-Q3) to achieve superior performance in downstream tasks. Our insights into existing solutions and the decoupled perspective for feasible integration of LLMs illuminate future research on visual reasoning techniques, especially LLM-assisted ones.