Zeyu Gao

Yao Mu, Tianxing Chen, Shijia Peng et al.

In the rapidly advancing field of robotics, dual-arm coordination and complex object manipulation are essential capabilities for developing advanced autonomous systems. However, the scarcity of diverse, high-quality demonstration data and real-world-aligned evaluation benchmarks severely limits such development. To address this, we introduce RoboTwin, a generative digital twin framework that uses 3D generative foundation models and large language models to produce diverse expert datasets and provide a real-world-aligned evaluation platform for dual-arm robotic tasks. Specifically, RoboTwin creates varied digital twins of objects from single 2D images, generating realistic and interactive scenarios. It also introduces a spatial relation-aware code generation framework that combines object annotations with large language models to break down tasks, determine spatial constraints, and generate precise robotic movement code. Our framework offers a comprehensive benchmark with both simulated and real-world data, enabling standardized evaluation and better alignment between simulated training and real-world performance. We validated our approach using the open-source COBOT Magic Robot platform. Policies pre-trained on RoboTwin-generated data and fine-tuned with limited real-world samples improve the success rate of over 70% for single-arm tasks and over 40% for dual-arm tasks compared to models trained solely on real-world data. This significant improvement demonstrates RoboTwin's potential to enhance the development and evaluation of dual-arm robotic manipulation systems. Project Page: https://robotwin-benchmark.github.io/early-version/.

Chunze Yang, Qidong Liu, Wenjie Zhao et al.

Whole-slide image visual question answering (WSI-VQA) frames pathology as an extreme-context search problem: to answer a free-form clinical query, a system must first navigate a gigapixel slide under a strict inspection budget to locate sparse, high-resolution evidence. Existing approaches largely fall into two paradigms: i) supervised pathology multimodal large language models (MLLMs) and agents can absorb localization and reasoning into learned modules, but they often couple navigation to task-specific supervision and retraining, limiting their practicality; ii) training-free pathology agents avoid this cost by keeping core models frozen, but often follow a question-first design, constructing the initial candidate set mainly from query-conditioned relevance. This can miss decisive morphology that is not named in the question, and force heavier inference-time scaffolding. To address this challenge, we introduce PathNavigate, a training-free pathology agent built around a scan-search-readout routine. Before question matching, PathNavigate scans the current slide at low magnification with a shared online memory module over frozen pathology features, producing a slide-specific surprise field that marks an abnormal-region pool. It then applies question-conditioned PLIP relevance only within this pool to select high-magnification search targets. Finally, it extracts local high-magnification evidence and answers with a frozen perceptor-adjudicator stack, using the same online memory as slide-level context. Experiments on WSI-VQA and SlideBench-BCNB show that the proposed scan-search-readout design improves answer accuracy and yields more interpretable evidence-selection trajectories with higher efficiency.The code is available online.

William McGough, Thomas Buddenkotte, Stephan Ursprung et al.

This study introduces an automated pipeline for renal cancer (RC) detection in non-contrast computed tomography (NCCT). In the development of our pipeline, we test three detections models: a shape model, a 2D-, and a 3D axial-sample model. Training (n=1348) and testing (n=64) data were gathered from open sources (KiTS23, Abdomen1k, CT-ORG) and Cambridge University Hospital (CUH). Results from cross-validation and testing revealed that the 2D axial sample model had the highest small ($\leq$40mm diameter) RC detection area under the curve (AUC) of 0.804. Our pipeline achieves 61.9\% sensitivity and 92.7\% specificity for small kidney cancers on unseen test data. Our results are much more accurate than previous attempts to automatically detect small renal cancers in NCCT, the most likely imaging modality for RC screening. This pipeline offers a promising advance that may enable screening for kidney cancers.

Wenyu Zhu, Hao Wang, Yuchen Zhou et al.

Binary Code Embedding (BCE) has important applications in various reverse engineering tasks such as binary code similarity detection, type recovery, control-flow recovery and data-flow analysis. Recent studies have shown that the Transformer model can comprehend the semantics of binary code to support downstream tasks. However, existing models overlooked the prior knowledge of assembly language. In this paper, we propose a novel Transformer-based approach, namely kTrans, to generate knowledge-aware binary code embedding. By feeding explicit knowledge as additional inputs to the Transformer, and fusing implicit knowledge with a novel pre-training task, kTrans provides a new perspective to incorporating domain knowledge into a Transformer framework. We inspect the generated embeddings with outlier detection and visualization, and also apply kTrans to 3 downstream tasks: Binary Code Similarity Detection (BCSD), Function Type Recovery (FTR) and Indirect Call Recognition (ICR). Evaluation results show that kTrans can generate high-quality binary code embeddings, and outperforms state-of-the-art (SOTA) approaches on downstream tasks by 5.2%, 6.8%, and 12.6% respectively. kTrans is publicly available at: https://github.com/Learner0x5a/kTrans-release

Jinye Qu, Zeyu Gao, Tielin Zhang et al.

Spiking Neural Networks (SNNs) have garnered widespread interest for their energy efficiency and brain-inspired event-driven properties. While recent methods like Spiking-YOLO have expanded the SNNs to more challenging object detection tasks, they often suffer from high latency and low detection accuracy, making them difficult to deploy on latency sensitive mobile platforms. Furthermore, the conversion method from Artificial Neural Networks (ANNs) to SNNs is hard to maintain the complete structure of the ANNs, resulting in poor feature representation and high conversion errors. To address these challenges, we propose two methods: timesteps compression and spike-time-dependent integrated (STDI) coding. The former reduces the timesteps required in ANN-SNN conversion by compressing information, while the latter sets a time-varying threshold to expand the information holding capacity. We also present a SNN-based ultra-low latency and high accurate object detection model (SUHD) that achieves state-of-the-art performance on nontrivial datasets like PASCAL VOC and MS COCO, with about remarkable 750x fewer timesteps and 30% mean average precision (mAP) improvement, compared to the Spiking-YOLO on MS COCO datasets. To the best of our knowledge, SUHD is the deepest spike-based object detection model to date that achieves ultra low timesteps to complete the lossless conversion.

Longfei Chen, Ji Zhao, Lanxiao Cui et al.

We introduce SecCodeBench-V2, a publicly released benchmark for evaluating Large Language Model (LLM) copilots' capabilities of generating secure code. SecCodeBench-V2 comprises 98 generation and fix scenarios derived from Alibaba Group's industrial productions, where the underlying security issues span 22 common CWE (Common Weakness Enumeration) categories across five programming languages: Java, C, Python, Go, and JavaScript. SecCodeBench-V2 adopts a function-level task formulation: each scenario provides a complete project scaffold and requires the model to implement or patch a designated target function under fixed interfaces and dependencies. For each scenario, SecCodeBench-V2 provides executable proof-of-concept (PoC) test cases for both functional validation and security verification. All test cases are authored and double-reviewed by security experts, ensuring high fidelity, broad coverage, and reliable ground truth. Beyond the benchmark itself, we build a unified evaluation pipeline that assesses models primarily via dynamic execution. For most scenarios, we compile and run model-generated artifacts in isolated environments and execute PoC test cases to validate both functional correctness and security properties. For scenarios where security issues cannot be adjudicated with deterministic test cases, we additionally employ an LLM-as-a-judge oracle. To summarize performance across heterogeneous scenarios and difficulty levels, we design a Pass@K-based scoring protocol with principled aggregation over scenarios and severity, enabling holistic and comparable evaluation across models. Overall, SecCodeBench-V2 provides a rigorous and reproducible foundation for assessing the security posture of AI coding assistants, with results and artifacts released at https://alibaba.github.io/sec-code-bench. The benchmark is publicly available at https://github.com/alibaba/sec-code-bench.

Jiusong Ge, Yingkang Zhan, Wenjie Zhao et al.

Traditional whole slide image (WSI) analysis methods typically rely on the multiple instance learning (MIL) paradigm, which extracts patch-level features at high magnification and aggregates them for slide-level prediction. However, such exhaustive patch-level processing is computationally expensive, severely limiting the efficiency and scalability of WSI analysis. To address this challenge, we propose PathCTM (a Pathology-oriented Continuous Thought Model) that enables token-efficient scale-space continuous reasoning for gigapixel WSIs. PathCTM formulates diagnostic inference as a dynamic sequential information pursuit. It progressively transitions from low-magnification global to high-magnification local inspection, and adaptively terminates inference when sufficient evidence is gathered to effectively bound decision uncertainty. Specifically, it uses conditional computation for dynamic scale switching with attention-guided region pruning, coupled with confidence-aware early stopping. Extensive experiments demonstrate that, compared with standard MIL-based methods, PathCTM reduces the number of required image patches by 95.95% and shortens inference time by approximately 95.62%, while maintaining AUC without degradation. Code is available at https://github.com/JSGe-AI/PathCTM.

Zeyu Gao, Yao Mu, Chen Chen et al.

End-to-end autonomous driving provides a feasible way to automatically maximize overall driving system performance by directly mapping the raw pixels from a front-facing camera to control signals. Recent advanced methods construct a latent world model to map the high dimensional observations into compact latent space. However, the latent states embedded by the world model proposed in previous works may contain a large amount of task-irrelevant information, resulting in low sampling efficiency and poor robustness to input perturbations. Meanwhile, the training data distribution is usually unbalanced, and the learned policy is challenging to cope with the corner cases during the driving process. To solve the above challenges, we present a SEMantic Masked recurrent world model (SEM2), which introduces a semantic filter to extract key driving-relevant features and make decisions via the filtered features, and is trained with a multi-source data sampler, which aggregates common data and multiple corner case data in a single batch, to balance the data distribution. Extensive experiments on CARLA show our method outperforms the state-of-the-art approaches in terms of sample efficiency and robustness to input permutations.

Francesca Fati, Felipe Coutinho, Marika Reinius et al.

Purpose. High-grade serous ovarian carcinoma (HGSOC) is characterized by pronounced biological and spatial heterogeneity and is frequently diagnosed at an advanced stage. Neoadjuvant chemotherapy (NACT) followed by delayed primary surgery is commonly employed in patients unsuitable for primary cytoreduction. The Chemotherapy Response Score (CRS) is a validated histopathological biomarker of response to NACT, but it is only available postoperatively. In this study, we investigate whether pre-treatment computed tomography (CT) imaging and clinical data can be used to predict CRS as an investigational decision-support adjunct to inform multidisciplinary team (MDT) discussions regarding expected treatment response. Methods. We proposed a 2.5D multimodal deep learning framework that processes lesion-dense omental slices using a pre-trained Vision Transformer encoder and integrates the resulting visual representations with clinical variables through an intermediate fusion module to predict CRS. Results. Our multimodal model, integrating imaging and clinical data, achieved a ROC-AUC of 0.95 alongside 95% accuracy and 80% precision on the internal test cohort (IEO, n=41 patients). On the external test set (OV04, n=70 patients), it achieved a ROC-AUC of 0.68, alongside 67% accuracy and 75% precision. Conclusion. These preliminary results demonstrate the feasibility of transformer-based deep learning for preoperative prediction of CRS in HGSOC using routine clinical data and CT imaging. As an investigational, pre-treatment decision-support tool, this approach may assist MDT discussions by providing early, non-invasive estimates of treatment response.

William Knottenbelt, William McGough, Rebecca Wray et al.

Motivation: Survival analysis is a branch of statistics that is crucial in medicine for modeling the time to critical events such as death or relapse, in order to improve treatment strategies and patient outcomes. Selecting survival models often involves a trade-off between performance and interpretability; deep learning models offer high performance but lack the transparency of more traditional approaches. This poses a significant issue in medicine, where practitioners are reluctant to use black-box models for critical patient decisions. Results: We introduce CoxKAN, a Cox proportional hazards Kolmogorov-Arnold Network for interpretable, high-performance survival analysis. Kolmogorov-Arnold Networks (KANs) were recently proposed as an interpretable and accurate alternative to multi-layer perceptrons. We evaluated CoxKAN on four synthetic and nine real datasets, including five cohorts with clinical data and four with genomics biomarkers. In synthetic experiments, CoxKAN accurately recovered interpretable hazard function formulae and excelled in automatic feature selection. Evaluations on real datasets showed that CoxKAN consistently outperformed the traditional Cox proportional hazards model (by up to 4% in C-index) and matched or surpassed the performance of deep learning-based models. Importantly, CoxKAN revealed complex interactions between predictor variables and uncovered symbolic formulae, which are key capabilities that other survival analysis methods lack, to provide clear insights into the impact of key biomarkers on patient risk. Availability and implementation: CoxKAN is available at GitHub and Zenodo

Inês P. Machado, Anna Reithmeir, Fryderyk Kogl et al.

High-grade serous ovarian carcinoma (HGSOC) is characterised by significant spatial and temporal heterogeneity, typically manifesting at an advanced metastatic stage. A major challenge in treating advanced HGSOC is effectively monitoring localised change in tumour burden across multiple sites during neoadjuvant chemotherapy (NACT) and predicting long-term pathological response and overall patient survival. In this work, we propose a self-supervised deformable image registration algorithm that utilises a general-purpose image encoder for image feature extraction to co-register contrast-enhanced computerised tomography scan images acquired before and after neoadjuvant chemotherapy. This approach addresses challenges posed by highly complex tumour deformations and longitudinal lesion matching during treatment. Localised tumour changes are calculated using the Jacobian determinant maps of the registration deformation at multiple disease sites and their macroscopic areas, including hypo-dense (i.e., cystic/necrotic), hyper-dense (i.e., calcified), and intermediate density (i.e., soft tissue) portions. A series of experiments is conducted to understand the role of a general-purpose image encoder and its application in quantifying change in tumour burden during neoadjuvant chemotherapy in HGSOC. This work is the first to demonstrate the feasibility of a self-supervised image registration approach in quantifying NACT-induced localised tumour changes across the whole disease burden of patients with complex multi-site HGSOC, which could be used as a potential marker for ovarian cancer patient's long-term pathological response and survival.

Zeyu Gao, Hao Wang, Yuchen Zhou et al.

As software becomes increasingly complex and prone to vulnerabilities, automated vulnerability detection is critically important, yet challenging. Given the significant successes of large language models (LLMs) in various tasks, there is growing anticipation of their efficacy in vulnerability detection. However, a quantitative understanding of their potential in vulnerability detection is still missing. To bridge this gap, we introduce a comprehensive vulnerability benchmark VulBench. This benchmark aggregates high-quality data from a wide range of CTF (Capture-the-Flag) challenges and real-world applications, with annotations for each vulnerable function detailing the vulnerability type and its root cause. Through our experiments encompassing 16 LLMs and 6 state-of-the-art (SOTA) deep learning-based models and static analyzers, we find that several LLMs outperform traditional deep learning approaches in vulnerability detection, revealing an untapped potential in LLMs. This work contributes to the understanding and utilization of LLMs for enhanced software security.

Yao Mu, Tianxing Chen, Zanxin Chen et al.

In the rapidly advancing field of robotics, dual-arm coordination and complex object manipulation are essential capabilities for developing advanced autonomous systems. However, the scarcity of diverse, high-quality demonstration data and real-world-aligned evaluation benchmarks severely limits such development. To address this, we introduce RoboTwin, a generative digital twin framework that uses 3D generative foundation models and large language models to produce diverse expert datasets and provide a real-world-aligned evaluation platform for dual-arm robotic tasks. Specifically, RoboTwin creates varied digital twins of objects from single 2D images, generating realistic and interactive scenarios. It also introduces a spatial relation-aware code generation framework that combines object annotations with large language models to break down tasks, determine spatial constraints, and generate precise robotic movement code. Our framework offers a comprehensive benchmark with both simulated and real-world data, enabling standardized evaluation and better alignment between simulated training and real-world performance. We validated our approach using the open-source COBOT Magic Robot platform. Policies pre-trained on RoboTwin-generated data and fine-tuned with limited real-world samples demonstrate significant potential for enhancing dual-arm robotic manipulation systems by improving success rates by over 70% for single-arm tasks and over 40% for dual-arm tasks compared to models trained solely on real-world data.

Hao Wang, Zeyu Gao, Chao Zhang et al.

Binary code representation learning has shown significant performance in binary analysis tasks. But existing solutions often have poor transferability, particularly in few-shot and zero-shot scenarios where few or no training samples are available for the tasks. To address this problem, we present CLAP (Contrastive Language-Assembly Pre-training), which employs natural language supervision to learn better representations of binary code (i.e., assembly code) and get better transferability. At the core, our approach boosts superior transfer learning capabilities by effectively aligning binary code with their semantics explanations (in natural language), resulting a model able to generate better embeddings for binary code. To enable this alignment training, we then propose an efficient dataset engine that could automatically generate a large and diverse dataset comprising of binary code and corresponding natural language explanations. We have generated 195 million pairs of binary code and explanations and trained a prototype of CLAP. The evaluations of CLAP across various downstream tasks in binary analysis all demonstrate exceptional performance. Notably, without any task-specific training, CLAP is often competitive with a fully supervised baseline, showing excellent transferability. We release our pre-trained model and code at https://github.com/Hustcw/CLAP.

Zeyu Gao, Hao Wang, Yuanda Wang et al.

Assembly code search is vital for reducing the burden on reverse engineers, allowing them to quickly identify specific functions using natural language within vast binary programs. Despite its significance, this critical task is impeded by the complexities involved in building high-quality datasets. This paper explores training a Large Language Model (LLM) to emulate a general compiler. By leveraging Ubuntu packages to compile a dataset of 20 billion tokens, we further continue pre-train CodeLlama as a Virtual Compiler (ViC), capable of compiling any source code of any language to assembly code. This approach allows for virtual compilation across a wide range of programming languages without the need for a real compiler, preserving semantic equivalency and expanding the possibilities for assembly code dataset construction. Furthermore, we use ViC to construct a sufficiently large dataset for assembly code search. Employing this extensive dataset, we achieve a substantial improvement in assembly code search performance, with our model surpassing the leading baseline by 26%.

Yuxin Cui, Zeyu Gao, Shuxian He et al.

Decompilation is foundational to binary analysis, yet conventional tools prioritize human readability over strict recompilability and verifiable runtime correctness. While recent LLM-based approaches attempt to refine decompiled pseudocode, they typically either optimize solely for readability or rely on static analysis for evaluation. This makes them prone to "semantic hallucinations" that compromise accuracy and fail to resolve actual runtime failures. For critical tasks like software modernization and vulnerability remediation, recovered code must not only compile but replicate the original binary's behavior. We present PCodeTrans, a feedback-driven framework that bridges the gap between decompilation, recompilation, and rigorous function-level dynamic validation. After extracting a minimal yet coherent context to guarantee recompilability, PCodeTrans employs an in situ substitutable engine to hot-swap the compiled function directly into the unmodified binary, natively preserving its authentic execution context and global dependencies. Guided by fine-grained differential tracing, PCodeTrans generates precise runtime feedback to iteratively guide an LLM in repairing semantic discrepancies. Evaluated on Coreutils and Binutils, PCodeTrans achieves unprecedented recovery performance when rectifying raw Hex-Rays outputs, attaining 100% function-level compilability on unstripped binaries alongside 99.55% and 99.89% test-validated behavioral consistency, respectively. In doing so, it resolves 76.56% and 79.74% of logic errors exposed by official test suites. Exhibiting exceptional resilience, PCodeTrans maintains over 96% behavioral consistency even on fully stripped binaries. By significantly outperforming all existing baselines, PCodeTrans paves a practical path to reliably translate decompiled pseudocode into compilable and executable equivalents.

Jiashuai Liu, Yingjia Shang, Yingkang Zhan et al.

With the widespread adoption of pathology foundation models in both research and clinical decision support systems, exploring their security has become a critical concern. However, despite their growing impact, the vulnerability of these models to adversarial attacks remains largely unexplored. In this work, we present the first systematic investigation into the security of pathology foundation models for whole slide image~(WSI) analysis against adversarial attacks. Specifically, we introduce the principle of \textit{local perturbation with global impact} and propose a label-free attack framework that operates without requiring access to downstream task labels. Under this attack framework, we revise four classical white-box attack methods and redefine the perturbation budget based on the characteristics of WSI. We conduct comprehensive experiments on three representative pathology foundation models across five datasets and six downstream tasks. Despite modifying only 0.1\% of patches per slide with imperceptible noise, our attack leads to downstream accuracy degradation that can reach up to 20\% in the worst cases. Furthermore, we analyze key factors that influence attack success, explore the relationship between patch-level vulnerability and semantic content, and conduct a preliminary investigation into potential defence strategies. These findings lay the groundwork for future research on the adversarial robustness and reliable deployment of pathology foundation models. Our code is publicly available at: https://github.com/Jiashuai-Liu-hmos/Attack-WSI-pathology-foundation-models.

Pargorn Puttapirat, Haichuan Zhang, Jingyi Deng et al.

Transition from conventional to digital pathology requires a new category of biomedical informatic infrastructure which could facilitate delicate pathological routine. Pathological diagnoses are sensitive to many external factors and is known to be subjective. Only systems that can meet strict requirements in pathology would be able to run along pathological routines and eventually digitized the study area, and the developed platform should comply with existing pathological routines and international standards. Currently, there are a number of available software tools which can perform histopathological tasks including virtual slide viewing, annotating, and basic image analysis, however, none of them can serve as a digital platform for pathology. Here we describe OpenHI2, an enhanced version Open Histopathological Image platform which is capable of supporting all basic pathological tasks and file formats; ready to be deployed in medical institutions on a standard server environment or cloud computing infrastructure. In this paper, we also describe the development decisions for the platform and propose solutions to overcome technical challenges so that OpenHI2 could be used as a platform for histopathological images. Further addition can be made to the platform since each component is modularized and fully documented. OpenHI2 is free, open-source, and available at https://gitlab.com/BioAI/OpenHI.

Kun Wu, Chengkai Hou, Jiaming Liu et al.

In this paper, we introduce RoboMIND (Multi-embodiment Intelligence Normative Data for Robot Manipulation), a dataset containing 107k demonstration trajectories across 479 diverse tasks involving 96 object classes. RoboMIND is collected through human teleoperation and encompasses comprehensive robotic-related information, including multi-view observations, proprioceptive robot state information, and linguistic task descriptions. To ensure data consistency and reliability for imitation learning, RoboMIND is built on a unified data collection platform and a standardized protocol, covering four distinct robotic embodiments: the Franka Emika Panda, the UR5e, the AgileX dual-arm robot, and a humanoid robot with dual dexterous hands. Our dataset also includes 5k real-world failure demonstrations, each accompanied by detailed causes, enabling failure reflection and correction during policy learning. Additionally, we created a digital twin environment in the Isaac Sim simulator, replicating the real-world tasks and assets, which facilitates the low-cost collection of additional training data and enables efficient evaluation. To demonstrate the quality and diversity of our dataset, we conducted extensive experiments using various imitation learning methods for single-task settings and state-of-the-art Vision-Language-Action (VLA) models for multi-task scenarios. By leveraging RoboMIND, the VLA models achieved high manipulation success rates and demonstrated strong generalization capabilities. To the best of our knowledge, RoboMIND is the largest multi-embodiment teleoperation dataset collected on a unified platform, providing large-scale and high-quality robotic training data. Our project is at https://x-humanoid-robomind.github.io/.

Fan Luo, Zeyu Gao, Xinhao Luo et al.

Spiking Neural Networks (SNNs), with their brain-inspired spatiotemporal dynamics and spike-driven computation, have emerged as promising energy-efficient alternatives to Artificial Neural Networks (ANNs). However, existing SNNs typically replicate inputs directly or aggregate them into frames at fixed intervals. Such strategies lead to neurons receiving nearly identical stimuli across time steps, severely limiting the model's expressive power, particularly in complex tasks like object detection. In this work, we propose the Temporal Dynamics Enhancer (TDE) to strengthen SNNs' capacity for temporal information modeling. TDE consists of two modules: a Spiking Encoder (SE) that generates diverse input stimuli across time steps, and an Attention Gating Module (AGM) that guides the SE generation based on inter-temporal dependencies. Moreover, to eliminate the high-energy multiplication operations introduced by the AGM, we propose a Spike-Driven Attention (SDA) to reduce attention-related energy consumption. Extensive experiments demonstrate that TDE can be seamlessly integrated into existing SNN-based detectors and consistently outperforms state-of-the-art methods, achieving mAP50-95 scores of 57.7% on the static PASCAL VOC dataset and 47.6% on the neuromorphic EvDET200K dataset. In terms of energy consumption, the SDA consumes only 0.240 times the energy of conventional attention modules.

Di Zhang, Zhangpeng Gong, Xiaobo Pang et al.

Foundation models have recently achieved impressive success in computational pathology, demonstrating strong generalization across diverse histopathology tasks. However, existing models overlook the heterogeneous and non-uniform organization of pathological regions of interest (ROIs) because they rely on natural image backbones not tailored for tissue morphology. Consequently, they often fail to capture the coherent tissue architecture beyond isolated patches, limiting interpretability and clinical relevance. To address these challenges, we present Cross-modal Adaptive Region Encoder (CARE), a foundation model for pathology that automatically partitions WSIs into several morphologically relevant regions. Specifically, CARE employs a two-stage pretraining strategy: (1) a self-supervised unimodal pretraining stage that learns morphological representations from 34,277 whole-slide images (WSIs) without segmentation annotations, and (2) a cross-modal alignment stage that leverages RNA and protein profiles to refine the construction and representation of adaptive regions. This molecular guidance enables CARE to identify biologically relevant patterns and generate irregular yet coherent tissue regions, selecting the most representative area as ROI. CARE supports a broad range of pathology-related tasks, using either the ROI feature or the slide-level feature obtained by aggregating adaptive regions. Based on only one-tenth of the pretraining data typically used by mainstream foundation models, CARE achieves superior average performance across 33 downstream benchmarks, including morphological classification, molecular prediction, and survival analysis, and outperforms other foundation model baselines overall.

Chengkai Hou, Yanjie Ze, Yankai Fu et al.

General visual representations learned from web-scale datasets for robotics have achieved great success in recent years, enabling data-efficient robot learning on manipulation tasks; yet these pre-trained representations are mostly on 2D images, neglecting the inherent 3D nature of the world. However, due to the scarcity of large-scale 3D data, it is still hard to extract a universal 3D representation from web datasets. Instead, we are seeking a general visual pre-training framework that could improve all 3D representations as an alternative. Our framework, called FVP, is a novel 4D Visual Pre-training framework for real-world robot learning. FVP frames the visual pre-training objective as a next-point-cloud-prediction problem, models the prediction model as a diffusion model, and pre-trains the model on the larger public datasets directly. Across twelve real-world manipulation tasks, FVP boosts the average success rate of 3D Diffusion Policy (DP3) for these tasks by 28%. The FVP pre-trained DP3 achieves state-of-the-art performance across imitation learning methods. Moreover, the efficacy of FVP adapts across various point cloud encoders and datasets. Finally, we apply FVP to the RDT-1B, a larger Vision-Language-Action robotic model, enhancing its performance on various robot tasks. Our project page is available at: https://4d-visual-pretraining.github.io/

Yi Niu, Jiashuai Liu, Yingkang Zhan et al.

Spatial Transcriptomics (ST) reveals the spatial distribution of gene expression in tissues, offering critical insights into biological processes and disease mechanisms. However, the high cost, limited coverage, and technical complexity of current ST technologies restrict their widespread use in clinical and research settings, making obtaining high-resolution transcriptomic profiles across large tissue areas challenging. Predicting ST from H\&E-stained histology images has emerged as a promising alternative to address these limitations but remains challenging due to the heterogeneous relationship between histomorphology and gene expression, which is affected by substantial variability across patients and tissue sections. In response, we propose PH2ST, a prompt-guided hypergraph learning framework, which leverages limited ST signals to guide multi-scale histological representation learning for accurate and robust spatial gene expression prediction. Extensive evaluations on two public ST datasets and multiple prompt sampling strategies simulating real-world scenarios demonstrate that PH2ST not only outperforms existing state-of-the-art methods, but also shows strong potential for practical applications such as imputing missing spots, ST super-resolution, and local-to-global prediction, highlighting its value for scalable and cost-effective spatial gene expression mapping in biomedical contexts.

Chengzu Li, Wenshan Wu, Huanyu Zhang et al. · cambridge

For human cognitive process, spatial reasoning and perception are closely entangled, yet the nature of this interplay remains underexplored in the evaluation of multimodal large language models (MLLMs). While recent MLLM advancements show impressive performance on reasoning, their capacity for human-like spatial cognition remains an open question. In this work, we introduce a systematic evaluation framework to assess the spatial reasoning abilities of state-of-the-art MLLMs relative to human performance. Central to our work is 11Plus-Bench, a high-quality benchmark derived from realistic standardized spatial aptitude tests. 11Plus-Bench also features fine-grained expert annotations of both perceptual complexity and reasoning process, enabling detailed instance-level analysis of model behavior. Through extensive experiments across 14 MLLMs and human evaluation, we find that current MLLMs exhibit early signs of spatial cognition. Despite a large performance gap compared to humans, MLLMs' cognitive profiles resemble those of humans in that cognitive effort correlates strongly with reasoning-related complexity. However, instance-level performance in MLLMs remains largely random, whereas human correctness is highly predictable and shaped by abstract pattern complexity. These findings highlight both emerging capabilities and limitations in current MLLMs' spatial reasoning capabilities and provide actionable insights for advancing model design.

Wen Wen, Tieliang Gong, Yunjiao Zhang et al.

Continual learning (CL) has emerged as a dominant paradigm for acquiring knowledge from sequential tasks while avoiding catastrophic forgetting. Although many CL methods have been proposed to show impressive empirical performance, the theoretical understanding of their generalization behavior remains limited, particularly for replay-based approaches. In this paper, we establish a unified theoretical framework for replay-based CL, deriving a series of information-theoretic bounds that explicitly characterize how the memory buffer interacts with the current task to affect generalization. Specifically, our hypothesis-based bounds reveal that utilizing the limited exemplars of previous tasks alongside the current task data, rather than exhaustive replay, facilitates improved generalization while effectively mitigating catastrophic forgetting. Furthermore, our prediction-based bounds yield tighter and computationally tractable upper bounds of the generalization gap through the use of low-dimensional variables. Our analysis is general and broadly applicable to a wide range of learning algorithms, exemplified by stochastic gradient Langevin dynamics (SGLD) as a representative method. Comprehensive experimental evaluations demonstrate the effectiveness of our derived bounds in capturing the generalization dynamics in replay-based CL settings.

Jipeng Li, Zeyu Gao, Yubin Qi et al.

Large Language Models (LLMs) have achieved remarkable performance across diverse tasks, yet their susceptibility to generating incorrect content during inference remains a critical unsolved challenge. While self-correction methods offer potential solutions, their effectiveness is hindered by two inherent limitations: (1) the absence of reliable guidance signals for error localization, and (2) the restricted reasoning depth imposed by conventional next-token decoding paradigms. To address these issues, we propose Feedback-Triggered Regeneration (FTR), a novel framework that synergizes user feedback with enhanced decoding dynamics. Specifically, FTR activates response regeneration only upon receiving negative user feedback, thereby circumventing error propagation from faulty self-assessment while preserving originally correct outputs. Furthermore, we introduce Long-Term Multipath (LTM) decoding, which enables systematic exploration of multiple reasoning trajectories through delayed sequence evaluation, effectively overcoming the myopic decision-making characteristic of standard next-token prediction. Extensive experiments on mathematical reasoning and code generation benchmarks demonstrate that our framework achieves consistent and significant improvements over state-of-the-art prompt-based self-correction methods.

Daniël Boeke, Cedrik Blommestijn, Rebecca N. Wray et al.

Recurrence risk estimation in clear cell renal cell carcinoma (ccRCC) is essential for guiding postoperative surveillance and treatment. The Leibovich score remains widely used for stratifying distant recurrence risk but offers limited patient-level resolution and excludes imaging information. This study evaluates multimodal recurrence prediction by integrating preoperative computed tomography (CT) and postoperative histopathology whole-slide images (WSIs). A modular deep learning framework with pretrained encoders and Cox-based survival modeling was tested across unimodal, late fusion, and intermediate fusion setups. In a real-world ccRCC cohort, WSI-based models consistently outperformed CT-only models, underscoring the prognostic strength of pathology. Intermediate fusion further improved performance, with the best model (TITAN-CONCH with ResNet-18) approaching the adjusted Leibovich score. Random tie-breaking narrowed the gap between the clinical baseline and learned models, suggesting discretization may overstate individualized performance. Using simple embedding concatenation, radiology added value primarily through fusion. These findings demonstrate the feasibility of foundation model-based multimodal integration for personalized ccRCC risk prediction. Future work should explore more expressive fusion strategies, larger multimodal datasets, and general-purpose CT encoders to better match pathology modeling capacity.

Siliang Qin, Fengrui Yang, Hao Wang et al.

Disassembly is a crucial yet challenging step in binary analysis. While emerging neural disassemblers show promise for efficiency and accuracy, they frequently generate outputs violating fundamental structural constraints, which significantly compromise their practical usability. To address this critical problem, we regularize the disassembly solution space by formalizing and applying key structural constraints based on post-dominance relations. This approach systematically detects widespread errors in existing neural disassemblers' outputs. These errors often originate from models' limited context modeling and instruction-level decoding that neglect global structural integrity. We introduce Tady, a novel neural disassembler featuring an improved model architecture and a dedicated post-processing algorithm, specifically engineered to address these deficiencies. Comprehensive evaluations on diverse binaries demonstrate that Tady effectively eliminates structural constraint violations and functions with high efficiency, while maintaining instruction-level accuracy.

Xuhang Chen, Ihsane Olakorede, Stefan Yu Bögli et al.

Artefacts compromise clinical decision-making in the use of medical time series. Pulsatile waveforms offer probabilities for accurate artefact detection, yet most approaches rely on supervised manners and overlook patient-level distribution shifts. To address these issues, we introduce a generalised label-free framework, GenClean, for real-time artefact cleaning and leverage an in-house dataset of 180,000 ten-second arterial blood pressure (ABP) samples for training. We first investigate patient-level generalisation, demonstrating robust performances under both intra- and inter-patient distribution shifts. We further validate its effectiveness through challenging cross-disease cohort experiments on the MIMIC-III database. Additionally, we extend our method to photoplethysmography (PPG), highlighting its applicability to diverse medical pulsatile signals. Finally, its integration into ICM+, a clinical research monitoring software, confirms the real-time feasibility of our framework, emphasising its practical utility in continuous physiological monitoring. This work provides a foundational step toward precision medicine in improving the reliability of high-resolution medical time series analysis

Wen Wen, Tieliang Gong, Yuxin Dong et al.

In recent years, information-theoretic generalization bounds have gained increasing attention for analyzing the generalization capabilities of meta-learning algorithms. However, existing results are confined to two-step bounds, failing to provide a sharper characterization of the meta-generalization gap that simultaneously accounts for environment-level and task-level dependencies. This paper addresses this fundamental limitation by developing a unified information-theoretic framework using a single-step derivation. The resulting meta-generalization bounds, expressed in terms of diverse information measures, exhibit substantial advantages over previous work, particularly in terms of tightness, scaling behavior associated with sampled tasks and samples per task, and computational tractability. Furthermore, through gradient covariance analysis, we provide new theoretical insights into the generalization properties of two classes of noisy and iterative meta-learning algorithms, where the meta-learner uses either the entire meta-training data (e.g., Reptile), or separate training and test data within the task (e.g., model agnostic meta-learning (MAML)). Numerical results validate the effectiveness of the derived bounds in capturing the generalization dynamics of meta-learning.

Zeyu Gao, Yao Mu, Jinye Qu et al.

Dual-arm robots offer enhanced versatility and efficiency over single-arm counterparts by enabling concurrent manipulation of multiple objects or cooperative execution of tasks using both arms. However, the coordination of dual-arm systems for long-horizon tasks continues to pose significant challenges, stemming from the intricate temporal and spatial dependencies among sub-tasks, necessitating intelligent decisions regarding the allocation of actions between arms and their optimal execution order. Existing task planning methods predominantly focus on single-arm robots or rely on predefined bimanual operations to use large language models (LLMs) generate task sequence with linear temporal dependency, failing to fully leverage the capabilities of dual-arm systems. To address this limitation, we introduce DAG-Plan, a structured task planning framework tailored for dual-arm robots. DAG-Plan harnesses LLMs to decompose intricate tasks into actionable sub-tasks represented as nodes within a directed acyclic graph (DAG). Critically, DAG-Plan dynamically assigns these sub-tasks to the appropriate arm based on real-time environmental observations, enabling parallel and adaptive execution. We evaluate DAG-Plan on the Dual-Arm Kitchen Benchmark, comprising 5 sequential tasks with 44 sub-tasks. Extensive experiments demonstrate the superiority of DAG-Plan over directly using LLM to generate linear task sequence, achieving 52.8% higher efficiency compared to the single-arm task planning and 48% higher success rate of the dual-arm task planning. Compared to iterative methods, DAG-Plan improving execution efficiency 84.1% due to its fewer query time. More demos and information are available on https://sites.google.com/view/dag-plan.

Jiangbo Shi, Chang Jia, Zeyu Gao et al.

Nuclei segmentation is a fundamental task in digital pathology analysis and can be automated by deep learning-based methods. However, the development of such an automated method requires a large amount of data with precisely annotated masks which is hard to obtain. Training with weakly labeled data is a popular solution for reducing the workload of annotation. In this paper, we propose a novel meta-learning-based nuclei segmentation method which follows the label correction paradigm to leverage data with noisy masks. Specifically, we design a fully conventional meta-model that can correct noisy masks using a small amount of clean meta-data. Then the corrected masks can be used to supervise the training of the segmentation model. Meanwhile, a bi-level optimization method is adopted to alternately update the parameters of the main segmentation model and the meta-model in an end-to-end way. Extensive experimental results on two nuclear segmentation datasets show that our method achieves the state-of-the-art result. It even achieves comparable performance with the model training on supervised data in some noisy settings.

Jialun Wu, Anyu Mao, Xinrui Bao et al.

Digital pathology plays a crucial role in the development of artificial intelligence in the medical field. The digital pathology platform can make the pathological resources digital and networked, and realize the permanent storage of visual data and the synchronous browsing processing without the limitation of time and space. It has been widely used in various fields of pathology. However, there is still a lack of an open and universal digital pathology platform to assist doctors in the management and analysis of digital pathological sections, as well as the management and structured description of relevant patient information. Most platforms cannot integrate image viewing, annotation and analysis, and text information management. To solve the above problems, we propose a comprehensive and extensible platform PIMIP. Our PIMIP has developed the image annotation functions based on the visualization of digital pathological sections. Our annotation functions support multi-user collaborative annotation and multi-device annotation, and realize the automation of some annotation tasks. In the annotation task, we invited a professional pathologist for guidance. We introduce a machine learning module for image analysis. The data we collected included public data from local hospitals and clinical examples. Our platform is more clinical and suitable for clinical use. In addition to image data, we also structured the management and display of text information. So our platform is comprehensive. The platform framework is built in a modular way to support users to add machine learning modules independently, which makes our platform extensible.

Jialun Wu, Yang Liu, Zeyu Gao et al.

Constructing large-scaled medical knowledge graphs can significantly boost healthcare applications for medical surveillance, bring much attention from recent research. An essential step in constructing large-scale MKG is extracting information from medical reports. Recently, information extraction techniques have been proposed and show promising performance in biomedical information extraction. However, these methods only consider limited types of entity and relation due to the noisy biomedical text data with complex entity correlations. Thus, they fail to provide enough information for constructing MKGs and restrict the downstream applications. To address this issue, we propose Biomedical Information Extraction, a hybrid neural network to extract relations from biomedical text and unstructured medical reports. Our model utilizes a multi-head attention enhanced graph convolutional network to capture the complex relations and context information while resisting the noise from the data. We evaluate our model on two major biomedical relationship extraction tasks, chemical-disease relation and chemical-protein interaction, and a cross-hospital pan-cancer pathology report corpus. The results show that our method achieves superior performance than baselines. Furthermore, we evaluate the applicability of our method under a transfer learning setting and show that BioIE achieves promising performance in processing medical text from different formats and writing styles.

Jialun Wu, Zeyu Gao, Haichuan Zhang et al.

Personalized diagnoses have not been possible due to sear amount of data pathologists have to bear during the day-to-day routine. This lead to the current generalized standards that are being continuously updated as new findings are reported. It is noticeable that these effective standards are developed based on a multi-source heterogeneous data, including whole-slide images and pathology and clinical reports. In this study, we propose a framework that combines pathological images and medical reports to generate a personalized diagnosis result for individual patient. We use nuclei-level image feature similarity and content-based deep learning method to search for a personalized group of population with similar pathological characteristics, extract structured prognostic information from descriptive pathology reports of the similar patient population, and assign importance of different prognostic factors to generate a personalized pathological diagnosis result. We use multi-source heterogeneous data from TCGA (The Cancer Genome Atlas) database. The result demonstrate that our framework matches the performance of pathologists in the diagnosis of renal cell carcinoma. This framework is designed to be generic, thus could be applied for other types of cancer. The weights could provide insights to the known prognostic factors and further guide more precise clinical treatment protocols.

Anyu Mao, Jialun Wu, Xinrui Bao et al.

Pathological diagnosis is the gold standard for cancer diagnosis, but it is labor-intensive, in which tasks such as cell detection, classification, and counting are particularly prominent. A common solution for automating these tasks is using nucleus segmentation technology. However, it is hard to train a robust nucleus segmentation model, due to several challenging problems, the nucleus adhesion, stacking, and excessive fusion with the background. Recently, some researchers proposed a series of automatic nucleus segmentation methods based on point annotation, which can significant improve the model performance. Nevertheless, the point annotation needs to be marked by experienced pathologists. In order to take advantage of segmentation methods based on point annotation, further alleviate the manual workload, and make cancer diagnosis more efficient and accurate, it is necessary to develop an automatic nucleus detection algorithm, which can automatically and efficiently locate the position of the nucleus in the pathological image and extract valuable information for pathologists. In this paper, we propose a W-shaped network for automatic nucleus detection. Different from the traditional U-Net based method, mapping the original pathology image to the target mask directly, our proposed method split the detection task into two sub-tasks. The first sub-task maps the original pathology image to the binary mask, then the binary mask is mapped to the density mask in the second sub-task. After the task is split, the task's difficulty is significantly reduced, and the network's overall performance is improved.

Jialun Wu, Haichuan Zhang, Zeyu Gao et al.

Diagnostic pathology, which is the basis and gold standard of cancer diagnosis, provides essential information on the prognosis of the disease and vital evidence for clinical treatment. Tumor region detection, subtype and grade classification are the fundamental diagnostic indicators for renal cell carcinoma (RCC) in whole-slide images (WSIs). However, pathological diagnosis is subjective, differences in observation and diagnosis between pathologists is common in hospitals with inadequate diagnostic capacity. The main challenge for developing deep learning based RCC diagnostic system is the lack of large-scale datasets with precise annotations. In this work, we proposed a deep learning-based framework for analyzing histopathological images of patients with renal cell carcinoma, which has the potential to achieve pathologist-level accuracy in diagnosis. A deep convolutional neural network (InceptionV3) was trained on the high-quality annotated dataset of The Cancer Genome Atlas (TCGA) whole-slide histopathological image for accurate tumor area detection, classification of RCC subtypes, and ISUP grades classification of clear cell carcinoma subtypes. These results suggest that our framework can help pathologists in the detection of cancer region and classification of subtypes and grades, which could be applied to any cancer type, providing auxiliary diagnosis and promoting clinical consensus.

Zeyu Gao, Bangyang Hong, Xianli Zhang et al.

Histological subtype of papillary (p) renal cell carcinoma (RCC), type 1 vs. type 2, is an essential prognostic factor. The two subtypes of pRCC have a similar pattern, i.e., the papillary architecture, yet some subtle differences, including cellular and cell-layer level patterns. However, the cellular and cell-layer level patterns almost cannot be captured by existing CNN-based models in large-size histopathological images, which brings obstacles to directly applying these models to such a fine-grained classification task. This paper proposes a novel instance-based Vision Transformer (i-ViT) to learn robust representations of histopathological images for the pRCC subtyping task by extracting finer features from instance patches (by cropping around segmented nuclei and assigning predicted grades). The proposed i-ViT takes top-K instances as input and aggregates them for capturing both the cellular and cell-layer level patterns by a position-embedding layer, a grade-embedding layer, and a multi-head multi-layer self-attention module. To evaluate the performance of the proposed framework, experienced pathologists are invited to selected 1162 regions of interest from 171 whole slide images of type 1 and type 2 pRCC. Experimental results show that the proposed method achieves better performance than existing CNN-based models with a significant margin.

Zeyu Gao, Jiangbo Shi, Xianli Zhang et al.

The grade of clear cell renal cell carcinoma (ccRCC) is a critical prognostic factor, making ccRCC nuclei grading a crucial task in RCC pathology analysis. Computer-aided nuclei grading aims to improve pathologists' work efficiency while reducing their misdiagnosis rate by automatically identifying the grades of tumor nuclei within histopathological images. Such a task requires precisely segment and accurately classify the nuclei. However, most of the existing nuclei segmentation and classification methods can not handle the inter-class similarity property of nuclei grading, thus can not be directly applied to the ccRCC grading task. In this paper, we propose a Composite High-Resolution Network for ccRCC nuclei grading. Specifically, we propose a segmentation network called W-Net that can separate the clustered nuclei. Then, we recast the fine-grained classification of nuclei to two cross-category classification tasks, based on two high-resolution feature extractors (HRFEs) which are proposed for learning these two tasks. The two HRFEs share the same backbone encoder with W-Net by a composite connection so that meaningful features for the segmentation task can be inherited for the classification task. Last, a head-fusion block is applied to generate the predicted label of each nucleus. Furthermore, we introduce a dataset for ccRCC nuclei grading, containing 1000 image patches with 70945 annotated nuclei. We demonstrate that our proposed method achieves state-of-the-art performance compared to existing methods on this large ccRCC grading dataset.

Zeyu Gao, Pargorn Puttapirat, Jiangbo Shi et al.

Obtaining a large amount of labeled data in medical imaging is laborious and time-consuming, especially for histopathology. However, it is much easier and cheaper to get unlabeled data from whole-slide images (WSIs). Semi-supervised learning (SSL) is an effective way to utilize unlabeled data and alleviate the need for labeled data. For this reason, we proposed a framework that employs an SSL method to accurately detect cancerous regions with a novel annotation method called Minimal Point-Based annotation, and then utilize the predicted results with an innovative hybrid loss to train a classification model for subtyping. The annotator only needs to mark a few points and label them are cancer or not in each WSI. Experiments on three significant subtypes of renal cell carcinoma (RCC) proved that the performance of the classifier trained with the Min-Point annotated dataset is comparable to a classifier trained with the segmentation annotated dataset for cancer region detection. And the subtyping model outperforms a model trained with only diagnostic labels by 12% in terms of f1-score for testing WSIs.

Jiangbo Shi, Zeyu Gao, Haichuan Zhang et al.

Pathological is crucial to cancer diagnosis. Usually, Pathologists draw their conclusion based on observed cell and tissue structure on histology slides. Rapid development in machine learning, especially deep learning have established robust and accurate classifiers. They are being used to analyze histopathological slides and assist pathologists in diagnosis. Most machine learning systems rely heavily on annotated data sets to gain experiences and knowledge to correctly and accurately perform various tasks such as classification and segmentation. This work investigates different granularity of annotations in histopathological data set including image-wise, bounding box, ellipse-wise, and pixel-wise to verify the influence of annotation in pathological slide on deep learning models. We design corresponding experiments to test classification and segmentation performance of deep learning models based on annotations with different annotation granularity. In classification, state-of-the-art deep learning-based classifiers perform better when trained by pixel-wise annotation dataset. On average, precision, recall and F1-score improves by 7.87%, 8.83% and 7.85% respectively. Thus, it is suggested that finer granularity annotations are better utilized by deep learning algorithms in classification tasks. Similarly, semantic segmentation algorithms can achieve 8.33% better segmentation accuracy when trained by pixel-wise annotations. Our study shows not only that finer-grained annotation can improve the performance of deep learning models, but also help extracts more accurate phenotypic information from histopathological slides. Intelligence systems trained on granular annotations may help pathologists inspecting certain regions for better diagnosis. The compartmentalized prediction approach similar to this work may contribute to phenotype and genotype association studies.