arXiv subjects

Yilan Zhang

Publications and source records attributed to Yilan Zhang.

16 recordsLinked to original sources

arXiv2026

VBVR-Pro: A Scalable and Verifiable Suite for Native Visual Reasoning

Native visual reasoning treats visual generation as the medium of reasoning itself: visual states (i.e. images and videos) are not merely inputs to be understood or outputs to be rendered, but first-class substrates for problem solving beyond language. Yet progress remains bottlenecked by the lack of scalable training tasks, reliable feedback, and controlled comparisons across generative substrates. In this work, we introduce VBVR-Pro, a closed-loop testbed that makes native visual reasoning through generation trainable, verifiable, optimizable, and experimentally controllable. 1) Task scaling. VBVR-Pro turns visual reasoning into a controlled task space of 300 procedurally generated tasks. Models trained on VBVR-Pro show strong transfer beyond the proposed suite across seven external visual reasoning benchmarks such as RISE-Video, MME-CoF-Pro, and BabyVision. 2) Verifiable rewards. VBVR-Pro provides verifiable reward scorers for task-grounded evaluation. Through a systematic study of leading MLLMs as judges, we identify recurring failure modes of the prevalent VLM-as-a-judge paradigm. In contrast, the proposed scorers are grounded in deterministic, task-specific rules, achieve fine-grained alignment with human judgments. Importantly, they serve as reliable reward signals for large-scale multi-task reinforcement learning and demonstrate stronger post-RL performance across visual reasoning tasks. 3) Mechanism study. VBVR-Pro enables controlled modality studies across more than 30 image, video, and interleaved generators. Our analysis shows that video generation remains strongest for tasks requiring persistent spatiotemporal state tracking, while interleaved generation provides a compute-efficient alternative. Critically, ablations and probing suggest the presence of vision-native trajectories that are crucial to visual reasoning. We release all data, models, scorers, and code.

cs.CV↗

arXiv2026

Perturb-and-Restore: Simulation-driven Structural Augmentation Framework for Imbalance Chromosomal Anomaly Detection

Detecting structural chromosomal abnormalities is crucial for accurate diagnosis and management of genetic disorders. However, collecting sufficient structural abnormality data is extremely challenging and costly in clinical practice, and not all abnormal types can be readily collected. As a result, deep learning approaches face significant performance degradation due to the severe imbalance and scarcity of abnormal chromosome data. To address this challenge, we propose a Perturb-and-Restore (P&R), a simulation-driven structural augmentation framework that effectively alleviates data imbalance in chromosome anomaly detection. The P&R framework comprises two key components: (1) Structure Perturbation and Restoration Simulation, which generates synthetic abnormal chromosomes by perturbing chromosomal banding patterns of normal chromosomes followed by a restoration diffusion network that reconstructs continuous chromosome content and edges, thus eliminating reliance on rare abnormal samples; and (2) Energy-guided Adaptive Sampling, an energy score-based online selection strategy that dynamically prioritizes high-quality synthetic samples by referencing the energy distribution of real samples. To evaluate our method, we construct a comprehensive structural anomaly dataset consisting of over 260,000 chromosome images, including 4,242 abnormal samples spanning 24 categories. Experimental results demonstrate that the P&R framework achieves state-of-the-art (SOTA) performance, surpassing existing methods with an average improvement of 8.92% in sensitivity, 8.89% in precision, and 13.79% in F1-score across all categories.

cs.CV↗

arXiv2025

Wearable-informed generative digital avatars predict task-conditioned post-stroke locomotion

Dynamic prediction of locomotor capacity after stroke could enable more individualized rehabilitation, yet current assessments largely provide static impairment scores and do not indicate whether patients can perform specific tasks such as slope walking or stair climbing. Here, we present a wearable-informed data-physics hybrid generative framework that reconstructs a stroke survivor's locomotor control from wearable inertial sensing and predicts task-conditioned post-stroke locomotion in new environments. From a single 20 m level-ground walking trial recorded by five IMUs, the framework personalizes a physics-based digital avatar using a healthy-motion prior and hybrid imitation learning, generating dynamically feasible, patient-specific movements for inclined walking and stair negotiation. Across 11 stroke inpatients, predicted postures reached 82.2% similarity for slopes and 69.9% for stairs, substantially exceeding a physics-only baseline. In a multicentre pilot randomized study (n = 21; 28 days), access to scenario-specific locomotion predictions to support task selection and difficulty titration was associated with larger gains in Fugl-Meyer lower-extremity scores than standard care (mean change 6.0 vs 3.7 points; $p < 0.05$). These results suggest that wearable-informed generative digital avatars may augment individualized gait rehabilitation planning and provide a pathway toward dynamically personalized post-stroke motor recovery strategies.

cs.CE↗

arXiv2025

Structural Prognostic Event Modeling for Multimodal Cancer Survival Analysis

The integration of histology images and gene profiles has shown great promise for improving survival prediction in cancer. However, current approaches often struggle to model intra- and inter-modal interactions efficiently and effectively due to the high dimensionality and complexity of the inputs. A major challenge is capturing critical prognostic events that, though few, underlie the complexity of the observed inputs and largely determine patient outcomes. These events, manifested as high-level structural signals such as spatial histologic patterns or pathway co-activations, are typically sparse, patient-specific, and unannotated, making them inherently difficult to uncover. To address this, we propose SlotSPE, a slot-based framework for structural prognostic event modeling. Specifically, inspired by the principle of factorial coding, we compress each patient's multimodal inputs into compact, modality-specific sets of mutually distinctive slots using slot attention. By leveraging these slot representations as encodings for prognostic events, our framework enables both efficient and effective modeling of complex intra- and inter-modal interactions, while also facilitating seamless incorporation of biological priors that enhance prognostic relevance. Extensive experiments on ten cancer benchmarks show that SlotSPE outperforms existing methods in 8 out of 10 cohorts, achieving an overall improvement of 2.9%. It remains robust under missing genomic data and delivers markedly improved interpretability through structured event decomposition.

cs.CV↗

arXiv2025

Using STAR-IRS to Secure Indoor Communications Through Symbol-Level Random Phase Modulation

This paper proposes a secure indoor communication scheme based on simultaneous transmitting and reflecting intelligent reflecting surface (STAR-IRS). Specifically, a transmitter (Alice) sends confidential information to its intended user (Bob) indoors, while several eavesdroppers (Eves) lurk outside. To safeguard the transmission from eavesdropping, the STAR-IRS is deployed on walls or windows. Upon impinging on the STAR-IRS, the incoming electromagnetic wave is dynamically partitioned into two components, enabling both transmission through and reflection from the surface. The reflected signal is controlled to enhance reception at Bob, while the transmitted signal is modulated with symbol-level random phase shifts to degrade the signal quality at Eves. Based on such a setting, the secrecy rate maximization problem is formulated. To solve it, a graph neural network (GNN)-based scheme is developed. Furthermore, a field-programmable gate array (FPGA)-based GNN accelerator is designed to reduce computational latency. Simulation results demonstrate that the proposed strategy outperforms both the conventional scheme and the reflection-only scheme in terms of secrecy performance. Moreover, the GNN-based approach achieves superior results compared to benchmark techniques such as maximum ratio transmission (MRT), zero forcing (ZF), and minimum mean square error (MMSE) in solving the optimization problem. Finally, experimental evaluations confirm that the FPGA-based accelerator enables low inference latency.

eess.SP↗

arXiv2025

PAST: A multimodal single-cell foundation model for histopathology and spatial transcriptomics in cancer

While pathology foundation models have transformed cancer image analysis, they often lack integration with molecular data at single-cell resolution, limiting their utility for precision oncology. Here, we present PAST, a pan-cancer single-cell foundation model trained on 20 million paired histopathology images and single-cell transcriptomes spanning multiple tumor types and tissue contexts. By jointly encoding cellular morphology and gene expression, PAST learns unified cross-modal representations that capture both spatial and molecular heterogeneity at the cellular level. This approach enables accurate prediction of single-cell gene expression, virtual molecular staining, and multimodal survival analysis directly from routine pathology slides. Across diverse cancers and downstream tasks, PAST consistently exceeds the performance of existing approaches, demonstrating robust generalizability and scalability. Our work establishes a new paradigm for pathology foundation models, providing a versatile tool for high-resolution spatial omics, mechanistic discovery, and precision cancer research.

q-bio.QM↗

arXiv2025

InternAgent: When Agent Becomes the Scientist -- Building Closed-Loop System from Hypothesis to Verification

Artificial Intelligence (AI) is accelerating the transformation of scientific research paradigms, not only enhancing research efficiency but also driving innovation. We introduce InternAgent, a unified closed-loop multi-agent framework to conduct Autonomous Scientific Research (ASR) across various scientific research fields, enabling researchers to tackle complicated problems in these fields with unprecedented speed and precision. InternAgent highlights three key advantages: 1) Scalability: InternAgent has demonstrated its versatility across 12 scientific research tasks, capable of generating innovative ideas to enhance the performance of baseline code. 2) Interactivity: InternAgent provides an interface for human expert feedback and multi-agent interaction in automated end-to-end processes, allowing for the seamless integration of domain expert knowledge. 3) Efficiency: InternAgent has achieved promising performance gains in several scientific fields with significantly less time cost compared to human efforts. For instance, in reaction yield prediction, it increased from 27.6% to 35.4% in just 12 hours; in enhancer activity prediction, accuracy rose from 0.65 to 0.79 with only 4 hours of processing; and in 2D semantic segmentation, precision advanced from 78.8% to 81.0% in a mere 30 hours.

cs.AI↗

arXiv2025

An Inclusive Foundation Model for Generalizable Cytogenetics in Precision Oncology

Chromosome analysis is vital for diagnosing genetic disorders and guiding cancer therapy decisions through the identification of somatic clonal aberrations. However, developing an AI model are hindered by the overwhelming complexity and diversity of chromosomal abnormalities, requiring extensive annotation efforts, while automated methods remain task-specific and lack generalizability due to the scarcity of comprehensive datasets spanning diverse resource conditions. Here, we introduce CHROMA, a foundation model for cytogenomics, designed to overcome these challenges by learning generalizable representations of chromosomal abnormalities. Pre-trained on over 84,000 specimens (~4 million chromosomal images) via self-supervised learning, CHROMA outperforms other methods across all types of abnormalities, even when trained on fewer labelled data and more imbalanced datasets. By facilitating comprehensive mapping of instability and clonal leisons across various aberration types, CHROMA offers a scalable and generalizable solution for reliable and automated clinical analysis, reducing the annotation workload for experts and advancing precision oncology through the early detection of rare genomic abnormalities, enabling broad clinical AI applications and making advanced genomic analysis more accessible.

q-bio.QM↗

arXiv2024

Improving Representation of High-frequency Components for Medical Visual Foundation Models

Foundation models have recently attracted significant attention for their impressive generalizability across diverse downstream tasks. However, these models are demonstrated to exhibit great limitations in representing high-frequency components and fine-grained details. In many medical imaging tasks, the precise representation of such information is crucial due to the inherently intricate anatomical structures, sub-visual features, and complex boundaries involved. Consequently, the limited representation of prevalent foundation models can result in significant performance degradation or even failure in these tasks. To address these challenges, we propose a novel pretraining strategy, named Frequency-advanced Representation Autoencoder (Frepa). Through high-frequency masking and low-frequency perturbation combined with adversarial learning, Frepa encourages the encoder to effectively represent and preserve high-frequency components in the image embeddings. Additionally, we introduce an innovative histogram-equalized image masking strategy, extending the Masked Autoencoder approach beyond ViT to other architectures such as Swin Transformer and convolutional networks. We develop Frepa across nine medical modalities and validate it on 32 downstream tasks for both 2D images and 3D volume data. Without fine-tuning, Frepa can outperform other self-supervised pretraining methods and, in some cases, even surpasses task-specific trained models. This improvement is particularly significant for tasks involving fine-grained details, such as achieving up to a +15% increase in DSC for retina vessel segmentation and a +7% increase in IoU for lung nodule detection. Further experiments quantitatively reveal that Frepa enables superior high-frequency representations and preservation in the embeddings, underscoring its potential for developing more generalized and universal medical image foundation models.

eess.IV↗

arXiv2024

Prototypical Information Bottlenecking and Disentangling for Multimodal Cancer Survival Prediction

Multimodal learning significantly benefits cancer survival prediction, especially the integration of pathological images and genomic data. Despite advantages of multimodal learning for cancer survival prediction, massive redundancy in multimodal data prevents it from extracting discriminative and compact information: (1) An extensive amount of intra-modal task-unrelated information blurs discriminability, especially for gigapixel whole slide images (WSIs) with many patches in pathology and thousands of pathways in genomic data, leading to an ``intra-modal redundancy" issue. (2) Duplicated information among modalities dominates the representation of multimodal data, which makes modality-specific information prone to being ignored, resulting in an ``inter-modal redundancy" issue. To address these, we propose a new framework, Prototypical Information Bottlenecking and Disentangling (PIBD), consisting of Prototypical Information Bottleneck (PIB) module for intra-modal redundancy and Prototypical Information Disentanglement (PID) module for inter-modal redundancy. Specifically, a variant of information bottleneck, PIB, is proposed to model prototypes approximating a bunch of instances for different risk levels, which can be used for selection of discriminative instances within modality. PID module decouples entangled multimodal data into compact distinct components: modality-common and modality-specific knowledge, under the guidance of the joint prototypical distribution. Extensive experiments on five cancer benchmark datasets demonstrated our superiority over other methods.

cs.CV↗

arXiv2023

Diffusion Models for Imperceptible and Transferable Adversarial Attack

Many existing adversarial attacks generate $L_p$-norm perturbations on image RGB space. Despite some achievements in transferability and attack success rate, the crafted adversarial examples are easily perceived by human eyes. Towards visual imperceptibility, some recent works explore unrestricted attacks without $L_p$-norm constraints, yet lacking transferability of attacking black-box models. In this work, we propose a novel imperceptible and transferable attack by leveraging both the generative and discriminative power of diffusion models. Specifically, instead of direct manipulation in pixel space, we craft perturbations in the latent space of diffusion models. Combined with well-designed content-preserving structures, we can generate human-insensitive perturbations embedded with semantic clues. For better transferability, we further "deceive" the diffusion model which can be viewed as an implicit recognition surrogate, by distracting its attention away from the target regions. To our knowledge, our proposed method, DiffAttack, is the first that introduces diffusion models into the adversarial attack field. Extensive experiments on various model structures, datasets, and defense methods have demonstrated the superiority of our attack over the existing attack methods.

cs.CV↗

arXiv2023

Dense Pixel-to-Pixel Harmonization via Continuous Image Representation

High-resolution (HR) image harmonization is of great significance in real-world applications such as image synthesis and image editing. However, due to the high memory costs, existing dense pixel-to-pixel harmonization methods are mainly focusing on processing low-resolution (LR) images. Some recent works resort to combining with color-to-color transformations but are either limited to certain resolutions or heavily depend on hand-crafted image filters. In this work, we explore leveraging the implicit neural representation (INR) and propose a novel image Harmonization method based on Implicit neural Networks (HINet), which to the best of our knowledge, is the first dense pixel-to-pixel method applicable to HR images without any hand-crafted filter design. Inspired by the Retinex theory, we decouple the MLPs into two parts to respectively capture the content and environment of composite images. A Low-Resolution Image Prior (LRIP) network is designed to alleviate the Boundary Inconsistency problem, and we also propose new designs for the training and inference process. Extensive experiments have demonstrated the effectiveness of our method compared with state-of-the-art methods. Furthermore, some interesting and practical applications of the proposed method are explored. Our code is available at https://github.com/WindVChen/INR-Harmonization.

cs.CV↗

arXiv2023

Zero-Shot Image Harmonization with Generative Model Prior

We propose a zero-shot approach to image harmonization, aiming to overcome the reliance on large amounts of synthetic composite images in existing methods. These methods, while showing promising results, involve significant training expenses and often struggle with generalization to unseen images. To this end, we introduce a fully modularized framework inspired by human behavior. Leveraging the reasoning capabilities of recent foundation models in language and vision, our approach comprises three main stages. Initially, we employ a pretrained vision-language model (VLM) to generate descriptions for the composite image. Subsequently, these descriptions guide the foreground harmonization direction of a text-to-image generative model (T2I). We refine text embeddings for enhanced representation of imaging conditions and employ self-attention and edge maps for structure preservation. Following each harmonization iteration, an evaluator determines whether to conclude or modify the harmonization direction. The resulting framework, mirroring human behavior, achieves harmonious results without the need for extensive training. We present compelling visual results across diverse scenes and objects, along with a user study validating the effectiveness of our approach.

cs.CV↗

arXiv2023

ECL: Class-Enhancement Contrastive Learning for Long-tailed Skin Lesion Classification

Skin image datasets often suffer from imbalanced data distribution, exacerbating the difficulty of computer-aided skin disease diagnosis. Some recent works exploit supervised contrastive learning (SCL) for this long-tailed challenge. Despite achieving significant performance, these SCL-based methods focus more on head classes, yet ignoring the utilization of information in tail classes. In this paper, we propose class-Enhancement Contrastive Learning (ECL), which enriches the information of minority classes and treats different classes equally. For information enhancement, we design a hybrid-proxy model to generate class-dependent proxies and propose a cycle update strategy for parameters optimization. A balanced-hybrid-proxy loss is designed to exploit relations between samples and proxies with different classes treated equally. Taking both "imbalanced data" and "imbalanced diagnosis difficulty" into account, we further present a balanced-weighted cross-entropy loss following curriculum learning schedule. Experimental results on the classification of imbalanced skin lesion data have demonstrated the superiority and effectiveness of our method.

cs.CV↗

arXiv2023

TFormer: A throughout fusion transformer for multi-modal skin lesion diagnosis

Multi-modal skin lesion diagnosis (MSLD) has achieved remarkable success by modern computer-aided diagnosis (CAD) technology based on deep convolutions. However, the information aggregation across modalities in MSLD remains challenging due to severity unaligned spatial resolution (e.g., dermoscopic image and clinical image) and heterogeneous data (e.g., dermoscopic image and patients' meta-data). Limited by the intrinsic local attention, most recent MSLD pipelines using pure convolutions struggle to capture representative features in shallow layers, thus the fusion across different modalities is usually done at the end of the pipelines, even at the last layer, leading to an insufficient information aggregation. To tackle the issue, we introduce a pure transformer-based method, which we refer to as ``Throughout Fusion Transformer (TFormer)'', for sufficient information integration in MSLD. Different from the existing approaches with convolutions, the proposed network leverages transformer as feature extraction backbone, bringing more representative shallow features. We then carefully design a stack of dual-branch hierarchical multi-modal transformer (HMT) blocks to fuse information across different image modalities in a stage-by-stage way. With the aggregated information of image modalities, a multi-modal transformer post-fusion (MTP) block is designed to integrate features across image and non-image data. Such a strategy that information of the image modalities is firstly fused then the heterogeneous ones enables us to better divide and conquer the two major challenges while ensuring inter-modality dynamics are effectively modeled.

cs.CV↗

arXiv2022

A Rotation Meanout Network with Invariance for Dermoscopy Image Classification and Retrieval

The computer-aided diagnosis (CAD) system can provide a reference basis for the clinical diagnosis of skin diseases. Convolutional neural networks (CNNs) can not only extract visual elements such as colors and shapes but also semantic features. As such they have made great improvements in many tasks of dermoscopy images. The imaging of dermoscopy has no principal orientation, indicating that there are a large number of skin lesion rotations in the datasets. However, CNNs lack rotation invariance, which is bound to affect the robustness of CNNs against rotations. To tackle this issue, we propose a rotation meanout (RM) network to extract rotation-invariant features from dermoscopy images. In RM, each set of rotated feature maps corresponds to a set of outputs of the weight-sharing convolutions and they are fused using meanout strategy to obtain the final feature maps. Through theoretical derivation, the proposed RM network is rotation-equivariant and can extract rotation-invariant features when followed by the global average pooling (GAP) operation. The extracted rotation-invariant features can better represent the original data in classification and retrieval tasks for dermoscopy images. The RM is a general operation, which does not change the network structure or increase any parameter, and can be flexibly embedded in any part of CNNs. Extensive experiments are conducted on a dermoscopy image dataset. The results show our method outperforms other anti-rotation methods and achieves great improvements in dermoscopy image classification and retrieval tasks, indicating the potential of rotation invariance in the field of dermoscopy images.

cs.CV↗