arXiv subjects

Jinxi Xiang

Publications and source records attributed to Jinxi Xiang.

At least 19 recordsLinked to original sources

arXiv2026

Not All Tokens Matter Equally: Dynamic In-context Vector Distillation with Decisive-Token Supervision for Long-form Medical Report Generation

Distilling demonstration effects into hidden-space interventions offers a lightweight alternative to full finetuning. However, existing multimodal variants are mostly evaluated on short-form tasks, where outputs end after a few tokens. Extending these methods to long-form generation exposes a fundamental yet underexamined limitation: token-level distillation implicitly treats all output tokens as equally informative, but long-form outputs are dominated by high-frequency template and grammatical tokens, while the tokens that actually determine output quality are sparsely distributed. In medical report generation (MRG), two such decisive tokens stand out: pathology-related tokens that determine diagnostic content, and the end-of-sequence (EOS) event that determines termination. Both receive insufficient supervision under uniform cross-entropy, and autoregressive decoding further compounds the problem by drifting away from teacher-forced trajectories. We propose DIVE, a frozen-backbone distillation framework that addresses long-form report generation through two complementary mechanisms matched to these failures. Decisive-token supervision restores supervision balance by upweighting the cross-entropy contribution of pathology-related tokens and the EOS event, ensuring that content fidelity and termination are learned during training rather than imposed at decoding time. State-conditioned dynamic steering replaces fixed open-loop residuals with hidden-state-dependent adapters, allowing the injected signal to adapt as decoding drifts. Experiments on MIMIC-CXR and CheXpert Plus with two medical VLM backbones show that DIVE consistently ranks among the strongest methods across lexical and clinical-proxy metrics. Our method achieves the best BLEU-4, ROUGE-L, and RadGraph F1 in all dataset--backbone settings, while remaining competitive on coarse label-level CheXbert F1.

cs.CL↗

arXiv2026

A Multimodal Foundation Model of Spatial Transcriptomics and Histology for Biological Discovery and Clinical Prediction

Spatial transcriptomics (ST) enables gene expression mapping within anatomical context but remains costly and low-throughput. Hematoxylin and eosin (H\&E) staining offers rich morphology yet lacks molecular resolution. We present \textbf{\ours} (\textbf{S}patial \textbf{T}ranscriptomics and hist\textbf{O}logy \textbf{R}epresentation \textbf{M}odel), a foundation model trained on 1.2 million spatially resolved transcriptomic profiles with matched histology across 18 organs. Using a hierarchical architecture integrating morphological features, gene expression, and spatial context, STORM bridges imaging and omics through robust molecular--morphological representations. STORM enhances spatial domain discovery, producing biologically coherent tissue maps, and outperforms existing methods in predicting spatial gene expression from H\&E images across 11 tumor types. The model is platform-agnostic, performing consistently across Visium, Xenium, Visium HD, and CosMx. Applied to 23 independent cohorts comprising 7,245 patients, STORM significantly improves immunotherapy response prediction and prognostication over established biomarkers, providing a scalable framework for spatially informed discovery and clinical precision medicine.

cs.AI↗

arXiv2026

A Generative Foundation Model for Multimodal Histopathology

Accurate diagnosis and treatment of complex diseases require integrating histological, molecular, and clinical data, yet in practice these modalities are often incomplete owing to tissue scarcity, assay cost, and workflow constraints. Existing computational approaches attempt to impute missing modalities from available data but rely on task-specific models trained on narrow, single source-target pairs, limiting their generalizability. Here we introduce MuPD (Multimodal Pathology Diffusion), a generative foundation model that embeds hematoxylin and eosin (H&E)-stained histology, molecular RNA profiles, and clinical text into a shared latent space through a diffusion transformer with decoupled cross-modal attention. Pretrained on 100 million histology image patches, 1.6 million text-histology pairs, and 10.8 million RNA-histology pairs spanning 34 human organs, MuPD supports diverse cross-modal synthesis tasks with minimal or no task-specific fine-tuning. For text-conditioned and image-to-image generation, MuPD synthesizes histologically faithful tissue architectures, reducing Fr\'echet inception distance (FID) scores by 50% relative to domain-specific models and improving few-shot classification accuracy by up to 47% through synthetic data augmentation. For RNA-conditioned histology generation, MuPD reduces FID by 23% compared with the next-best method while preserving cell-type distributions across five cancer types. As a virtual stainer, MuPD translates H&E images to immunohistochemistry and multiplex immunofluorescence, improving average marker correlation by 37% over existing approaches. These results demonstrate that a single, unified generative model pretrained across heterogeneous pathology modalities can substantially outperform specialized alternatives, providing a scalable computational framework for multimodal histopathology.

cs.CV↗

arXiv2025

nnMIL: A generalizable multiple instance learning framework for computational pathology

Computational pathology holds substantial promise for improving diagnosis and guiding treatment decisions. Recent pathology foundation models enable the extraction of rich patch-level representations from large-scale whole-slide images (WSIs), but current approaches for aggregating these features into slide-level predictions remain constrained by design limitations that hinder generalizability and reliability. Here we present nnMIL, a simple yet broadly applicable multiple-instance learning framework that connects patch-level foundation models to robust slide-level clinical prediction. nnMIL introduces random sampling at both the patch and feature levels, enabling large-batch optimization, task-aware sampling strategies, and efficient and scalable training across datasets and model architectures. A lightweight aggregator performs sliding-window inference to generate ensemble slide-level predictions and supports principled uncertainty estimation. Across 40,000 WSIs encompassing 35 clinical tasks and four pathology foundation models, nnMIL consistently outperformed existing MIL methods for disease diagnosis, histologic subtyping, molecular biomarker detection, and pan-cancer prognosis prediction. It further demonstrated strong cross-model generalization, reliable uncertainty quantification, and robust survival stratification in multiple external cohorts. In conclusion, nnMIL offers a practical and generalizable solution for translating pathology foundation models into clinically meaningful predictions, advancing the development and deployment of reliable AI systems in real-world settings.

cs.CV↗

arXiv2025

Ensemble learning of pathology foundation models for precision oncology

Histopathology is essential for cancer diagnosis and treatment selection, and pathology foundation models learn visual representations from whole-slide images (WSIs). However, existing foundation models are trained on disparate datasets using varying strategies, leading to inconsistent performance and limited generalizability. Here, we introduce ELF (Ensemble Learning of Foundation models), which integrates five pretrained pathology foundation models into unified slide-level representations. Trained on 53,699 WSIs spanning 20 anatomical sites, ELF leverages ensemble learning to capture complementary information across models. ELF's slide-level architecture is designed for data-efficient downstream evaluation, including settings with limited data such as therapeutic response prediction. We evaluate ELF for disease classification, biomarker detection, as well as anticancer and immunotherapy response prediction across multiple cancer types. ELF achieves higher performance than the evaluated constituent and slide-level foundation models across the tested tasks, supporting further evaluation of ensemble learning for pathology applications in oncology.

cs.CV↗

arXiv2023

Image Super-resolution Via Latent Diffusion: A Sampling-space Mixture Of Experts And Frequency-augmented Decoder Approach

The recent use of diffusion prior, enhanced by pre-trained text-image models, has markedly elevated the performance of image super-resolution (SR). To alleviate the huge computational cost required by pixel-based diffusion SR, latent-based methods utilize a feature encoder to transform the image and then implement the SR image generation in a compact latent space. Nevertheless, there are two major issues that limit the performance of latent-based diffusion. First, the compression of latent space usually causes reconstruction distortion. Second, huge computational cost constrains the parameter scale of the diffusion model. To counteract these issues, we first propose a frequency compensation module that enhances the frequency components from latent space to pixel space. The reconstruction distortion (especially for high-frequency information) can be significantly decreased. Then, we propose to use Sample-Space Mixture of Experts (SS-MoE) to achieve more powerful latent-based SR, which steadily improves the capacity of the model without a significant increase in inference costs. These carefully crafted designs contribute to performance improvements in largely explored 4x blind super-resolution benchmarks and extend to large magnification factors, i.e., 8x image SR benchmarks. The code is available at https://github.com/amandaluof/moe_sr.

cs.CV↗

arXiv2023

Effortless Cross-Platform Video Codec: A Codebook-Based Method

Under certain circumstances, advanced neural video codecs can surpass the most complex traditional codecs in their rate-distortion (RD) performance. One of the main reasons for the high performance of existing neural video codecs is the use of the entropy model, which can provide more accurate probability distribution estimations for compressing the latents. This also implies the rigorous requirement that entropy models running on different platforms should use consistent distribution estimations. However, in cross-platform scenarios, entropy models running on different platforms usually yield inconsistent probability distribution estimations due to floating point computation errors that are platform-dependent, which can cause the decoding side to fail in correctly decoding the compressed bitstream sent by the encoding side. In this paper, we propose a cross-platform video compression framework based on codebooks, which avoids autoregressive entropy modeling and achieves video compression by transmitting the index sequence of the codebooks. Moreover, instead of using optical flow for context alignment, we propose to use the conditional cross-attention module to obtain the context between frames. Due to the absence of autoregressive modeling and optical flow alignment, we can design an extremely minimalist framework that can greatly benefit computational efficiency. Importantly, our framework no longer contains any distribution estimation modules for entropy modeling, and thus computations across platforms are not necessarily consistent. Experimental results show that our method can outperform the traditional H.265 (medium) even without any entropy constraints, while achieving the cross-platform property intrinsically.

cs.CV↗

arXiv2023

Towards Real-Time Neural Video Codec for Cross-Platform Application Using Calibration Information

The state-of-the-art neural video codecs have outperformed the most sophisticated traditional codecs in terms of RD performance in certain cases. However, utilizing them for practical applications is still challenging for two major reasons. 1) Cross-platform computational errors resulting from floating point operations can lead to inaccurate decoding of the bitstream. 2) The high computational complexity of the encoding and decoding process poses a challenge in achieving real-time performance. In this paper, we propose a real-time cross-platform neural video codec, which is capable of efficiently decoding of 720P video bitstream from other encoding platforms on a consumer-grade GPU. First, to solve the problem of inconsistency of codec caused by the uncertainty of floating point calculations across platforms, we design a calibration transmitting system to guarantee the consistent quantization of entropy parameters between the encoding and decoding stages. The parameters that may have transboundary quantization between encoding and decoding are identified in the encoding stage, and their coordinates will be delivered by auxiliary transmitted bitstream. By doing so, these inconsistent parameters can be processed properly in the decoding stage. Furthermore, to reduce the bitrate of the auxiliary bitstream, we rectify the distribution of entropy parameters using a piecewise Gaussian constraint. Second, to match the computational limitations on the decoding side for real-time video codec, we design a lightweight model. A series of efficiency techniques enable our model to achieve 25 FPS decoding speed on NVIDIA RTX 2080 GPU. Experimental results demonstrate that our model can achieve real-time decoding of 720P videos while encoding on another platform. Furthermore, the real-time model brings up to a maximum of 24.2\% BD-rate improvement from the perspective of PSNR with the anchor H.265.

cs.CV↗

arXiv2023

Dynamic Low-Rank Instance Adaptation for Universal Neural Image Compression

The latest advancements in neural image compression show great potential in surpassing the rate-distortion performance of conventional standard codecs. Nevertheless, there exists an indelible domain gap between the datasets utilized for training (i.e., natural images) and those utilized for inference (e.g., artistic images). Our proposal involves a low-rank adaptation approach aimed at addressing the rate-distortion drop observed in out-of-domain datasets. Specifically, we perform low-rank matrix decomposition to update certain adaptation parameters of the client's decoder. These updated parameters, along with image latents, are encoded into a bitstream and transmitted to the decoder in practical scenarios. Due to the low-rank constraint imposed on the adaptation parameters, the resulting bit rate overhead is small. Furthermore, the bit rate allocation of low-rank adaptation is \emph{non-trivial}, considering the diverse inputs require varying adaptation bitstreams. We thus introduce a dynamic gating network on top of the low-rank adaptation method, in order to decide which decoder layer should employ adaptation. The dynamic adaptation network is optimized end-to-end using rate-distortion loss. Our proposed method exhibits universality across diverse image datasets. Extensive results demonstrate that this paradigm significantly mitigates the domain gap, surpassing non-adaptive methods with an average BD-rate improvement of approximately $19\%$ across out-of-domain images. Furthermore, it outperforms the most advanced instance adaptive methods by roughly $5\%$ BD-rate. Ablation studies confirm our method's ability to universally enhance various image compression architectures.

eess.IV↗

arXiv2023

CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting

Nuclear detection, segmentation and morphometric profiling are essential in helping us further understand the relationship between histology and patient outcome. To drive innovation in this area, we setup a community-wide challenge using the largest available dataset of its kind to assess nuclear segmentation and cellular composition. Our challenge, named CoNIC, stimulated the development of reproducible algorithms for cellular recognition with real-time result inspection on public leaderboards. We conducted an extensive post-challenge analysis based on the top-performing models using 1,658 whole-slide images of colon tissue. With around 700 million detected nuclei per model, associated features were used for dysplasia grading and survival analysis, where we demonstrated that the challenge's improvement over the previous state-of-the-art led to significant boosts in downstream performance. Our findings also suggest that eosinophils and neutrophils play an important role in the tumour microevironment. We release challenge models and WSI-level results to foster the development of further methods for biomarker discovery.

cs.CV↗

arXiv2023

Federated attention consistent learning models for prostate cancer diagnosis and Gleason grading

Artificial intelligence (AI) holds significant promise in transforming medical imaging, enhancing diagnostics, and refining treatment strategies. However, the reliance on extensive multicenter datasets for training AI models poses challenges due to privacy concerns. Federated learning provides a solution by facilitating collaborative model training across multiple centers without sharing raw data. This study introduces a federated attention-consistent learning (FACL) framework to address challenges associated with large-scale pathological images and data heterogeneity. FACL enhances model generalization by maximizing attention consistency between local clients and the server model. To ensure privacy and validate robustness, we incorporated differential privacy by introducing noise during parameter transfer. We assessed the effectiveness of FACL in cancer diagnosis and Gleason grading tasks using 19,461 whole-slide images of prostate cancer from multiple centers. In the diagnosis task, FACL achieved an area under the curve (AUC) of 0.9718, outperforming seven centers with an average AUC of 0.9499 when categories are relatively balanced. For the Gleason grading task, FACL attained a Kappa score of 0.8463, surpassing the average Kappa score of 0.7379 from six centers. In conclusion, FACL offers a robust, accurate, and cost-effective AI training model for prostate cancer pathology while maintaining effective data safeguards.

cs.CV↗

arXiv2023

Artificial intelligence for diagnosing and predicting survival of patients with renal cell carcinoma: Retrospective multi-center study

Background: Clear cell renal cell carcinoma (ccRCC) is the most common renal-related tumor with high heterogeneity. There is still an urgent need for novel diagnostic and prognostic biomarkers for ccRCC. Methods: We proposed a weakly-supervised deep learning strategy using conventional histology of 1752 whole slide images from multiple centers. Our study was demonstrated through internal cross-validation and external validations for the deep learning-based models. Results: Automatic diagnosis for ccRCC through intelligent subtyping of renal cell carcinoma was proved in this study. Our graderisk achieved aera the curve (AUC) of 0.840 (95% confidence interval: 0.805-0.871) in the TCGA cohort, 0.840 (0.805-0.871) in the General cohort, and 0.840 (0.805-0.871) in the CPTAC cohort for the recognition of high-grade tumor. The OSrisk for the prediction of 5-year survival status achieved AUC of 0.784 (0.746-0.819) in the TCGA cohort, which was further verified in the independent General cohort and the CPTAC cohort, with AUC of 0.774 (0.723-0.820) and 0.702 (0.632-0.765), respectively. Cox regression analysis indicated that graderisk, OSrisk, tumor grade, and tumor stage were found to be independent prognostic factors, which were further incorporated into the competing-risk nomogram (CRN). Kaplan-Meier survival analyses further illustrated that our CRN could significantly distinguish patients with high survival risk, with hazard ratio of 5.664 (3.893-8.239, p < 0.0001) in the TCGA cohort, 35.740 (5.889-216.900, p < 0.0001) in the General cohort and 6.107 (1.815 to 20.540, p < 0.0001) in the CPTAC cohort. Comparison analyses conformed that our CRN outperformed current prognosis indicators in the prediction of survival status, with higher concordance index for clinical prognosis.

eess.IV↗

arXiv2022

Deep learning-based approach to reveal tumor mutational burden status from whole slide images across multiple cancer types

Tumor mutational burden (TMB) is a potential genomic biomarker of immunotherapy. However, TMB detected through whole exome sequencing lacks clinical penetration in low-resource settings. In this study, we proposed a multi-scale deep learning framework to address the detection of TMB status from routinely used whole slide images for a multiple cancer TMB prediction model (MC- TMB). The MC-TMB achieved a mean area under the curve (AUC) of 0.818 (0.804-0.831) in the cross-validation cohort, which showed superior performance to each single-scale model. The improvements of MC-TMB over the single-tumor models were also confirmed by the ablation tests on x10 magnification, and the highly concerned regions typically correspond to dense lymphocytic infiltration and heteromorphic tumor cells. MC-TMB algorithm also exhibited good generalization on the external validation cohort with an AUC of 0.732 (0.683-0.761), and better performance when compared to other methods. In conclusion, we proposed a deep learning-based approach to reveal tumor mutational burden status from routinely used pathological slides across multiple cancer types.

cs.CV↗

arXiv2022

A Deep Learning Framework for Nuclear Segmentation and Classification in Histopathological Images

Nucleus segmentation and classification are the prerequisites in the workflow of digital pathology processing. However, it is very challenging due to its high-level heterogeneity and wide variations. This work proposes a deep neural network to simultaneously achieve nuclear classification and segmentation, which is designed using a unified framework with three different branches, including segmentation, HoVer mapping, and classification. The segmentation branch aims to generate the boundaries of each nucleus. The HoVer branch calculates the horizontal and vertical distances of nuclear pixels to their centres of mass. The nuclear classification branch is used to distinguish the class of pixels inside the nucleus obtained from segmentation.

eess.IV↗

arXiv2021

Self-Ensembling Contrastive Learning for Semi-Supervised Medical Image Segmentation

Deep learning has demonstrated significant improvements in medical image segmentation using a sufficiently large amount of training data with manual labels. Acquiring well-representative labels requires expert knowledge and exhaustive labors. In this paper, we aim to boost the performance of semi-supervised learning for medical image segmentation with limited labels using a self-ensembling contrastive learning technique. To this end, we propose to train an encoder-decoder network at image-level with small amounts of labeled images, and more importantly, we learn latent representations directly at feature-level by imposing contrastive loss on unlabeled images. This method strengthens intra-class compactness and inter-class separability, so as to get a better pixel classifier. Moreover, we devise a student encoder for online learning and an exponential moving average version of it, called teacher encoder, to improve the performance iteratively in a self-ensembling manner. To construct contrastive samples with unlabeled images, two sampling strategies that exploit structure similarity across medical images and utilize pseudo-labels for construction, termed region-aware and anatomical-aware contrastive sampling, are investigated. We conduct extensive experiments on an MRI and a CT segmentation dataset and demonstrate that in a limited label setting, the proposed method achieves state-of-the-art performance. Moreover, the anatomical-aware strategy that prepares contrastive samples on-the-fly using pseudo-labels realizes better contrastive regularization on feature representations.

cs.CV↗

arXiv2021

MMV-Net: A Multiple Measurement Vector Network for Multi-frequency Electrical Impedance Tomography

Multi-frequency Electrical Impedance Tomography (mfEIT) is an emerging biomedical imaging modality to reveal frequency-dependent conductivity distributions in biomedical applications. Conventional model-based image reconstruction methods suffer from low spatial resolution, unconstrained frequency correlation and high computational cost. Deep learning has been extensively applied in solving the EIT inverse problem in biomedical and industrial process imaging. However, most existing learning-based approaches deal with the single-frequency setup, which is inefficient and ineffective when extended to address the multi-frequency setup. In this paper, we present a Multiple Measurement Vector (MMV) model based learning algorithm named MMV-Net to solve the mfEIT image reconstruction problem. MMV-Net takes into account the correlations between mfEIT images and unfolds the update steps of the Alternating Direction Method of Multipliers (ADMM) for the MMV problem. The non-linear shrinkage operator associated with the weighted l2_1 regularization term is generalized with a cascade of a Spatial Self-Attention module and a Convolutional Long Short-Term Memory (ConvLSTM) module to capture intra- and inter-frequency dependencies. The proposed MMVNet was validated on our Edinburgh mfEIT Dataset and a series of comprehensive experiments. All reconstructed results show superior image quality, convergence performance and noise robustness against the state of the art.

eess.IV↗

arXiv2021

FISTA-Net: Learning A Fast Iterative Shrinkage Thresholding Network for Inverse Problems in Imaging

Inverse problems are essential to imaging applications. In this paper, we propose a model-based deep learning network, named FISTA-Net, by combining the merits of interpretability and generality of the model-based Fast Iterative Shrinkage/Thresholding Algorithm (FISTA) and strong regularization and tuning-free advantages of the data-driven neural network. By unfolding the FISTA into a deep network, the architecture of FISTA-Net consists of multiple gradient descent, proximal mapping, and momentum modules in cascade. Different from FISTA, the gradient matrix in FISTA-Net can be updated during iteration and a proximal operator network is developed for nonlinear thresholding which can be learned through end-to-end training. Key parameters of FISTA-Net including the gradient step size, thresholding value and momentum scalar are tuning-free and learned from training data rather than hand-crafted. We further impose positive and monotonous constraints on these parameters to ensure they converge properly. The experimental results, evaluated both visually and quantitatively, show that the FISTA-Net can optimize parameters for different imaging tasks, i.e. Electromagnetic Tomography (EMT) and X-ray Computational Tomography (X-ray CT). It outperforms the state-of-the-art model-based and deep learning methods and exhibits good generalization ability over other competitive learning-based approaches under different noise levels.

eess.IV↗

arXiv2020

Multi-frequency Electromagnetic Tomography for Acute Stroke Detection Using Frequency Constrained Sparse Bayesian Learning

Imaging the bio-impedance distribution of the brain can provide initial diagnosis of acute stroke. This paper presents a compact and non-radiative tomographic modality, i.e. multi-frequency Electromagnetic Tomography (mfEMT), for the initial diagnosis of acute stroke. The mfEMT system consists of 12 channels of gradiometer coils with adjustable sensitivity and excitation frequency. To solve the image reconstruction problem of mfEMT, we propose an enhanced Frequency-Constrained Sparse Bayesian Learning (FC-SBL) to simultaneously reconstruct the conductivity distribution at all frequencies. Based on the Multiple Measurement Vector (MMV) model in the Sparse Bayesian Learning (SBL) framework, FC-SBL can recover the underlying distribution pattern of conductivity among multiple images by exploiting the frequency constraint information. A realistic 3D head model was established to simulate stroke detection scenarios, showing the capability of mfEMT to penetrate the highly resistive skull and improved image quality with FC-SBL. Both simulations and experiments showed that the proposed FC-SBL method is robust to noisy data for image reconstruction problems of mfEMT compared to the single measurement vector model, which is promising to detect acute strokes in the brain region with enhanced spatial resolution and in a baseline-free manner.

physics.app-ph↗