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.

Structure-aware Semantic Discrepancy and Consistency for 3D Medical Image Self-supervised Learning

3D medical image self-supervised learning (mSSL) holds great promise for medical analysis. Effectively supporting broader applications requires considering anatomical structure variations in location, scale, and morphology, which are crucial for capturing meaningful distinctions. However, previous mSSL methods partition images with fixed-size patches, often ignoring the structure variations. In this work, we introduce a novel perspective on 3D medical images with the goal of learning structure-aware representations. We assume that patches within the same structure share the same semantics (semantic consistency) while those from different structures exhibit distinct semantics (semantic discrepancy). Based on this assumption, we propose an mSSL framework named $S^2DC$, achieving Structure-aware Semantic Discrepancy and Consistency in two steps. First, $S^2DC$ enforces distinct representations for different patches to increase semantic discrepancy by leveraging an optimal transport strategy. Second, $S^2DC$ advances semantic consistency at the structural level based on neighborhood similarity distribution. By bridging patch-level and structure-level representations, $S^2DC$ achieves structure-aware representations. Thoroughly evaluated across 10 datasets, 4 tasks, and 3 modalities, our proposed method consistently outperforms the state-of-the-art methods in mSSL.

A Gift from the Integration of Discriminative and Diffusion-based Generative Learning: Boundary Refinement Remote Sensing Semantic Segmentation

Remote sensing semantic segmentation must address both what the ground objects are within an image and where they are located. Consequently, segmentation models must ensure not only the semantic correctness of large-scale patches (low-frequency information) but also the precise localization of boundaries between patches (high-frequency information). However, most existing approaches rely heavily on discriminative learning, which excels at capturing low-frequency features, while overlooking its inherent limitations in learning high-frequency features for semantic segmentation. Recent studies have revealed that diffusion generative models excel at generating high-frequency details. Our theoretical analysis confirms that the diffusion denoising process significantly enhances the model's ability to learn high-frequency features; however, we also observe that these models exhibit insufficient semantic inference for low-frequency features when guided solely by the original image. Therefore, we integrate the strengths of both discriminative and generative learning, proposing the Integration of Discriminative and diffusion-based Generative learning for Boundary Refinement (IDGBR) framework. The framework first generates a coarse segmentation map using a discriminative backbone model. This map and the original image are fed into a conditioning guidance network to jointly learn a guidance representation subsequently leveraged by an iterative denoising diffusion process refining the coarse segmentation. Extensive experiments across five remote sensing semantic segmentation datasets (binary and multi-class segmentation) confirm our framework's capability of consistent boundary refinement for coarse results from diverse discriminative architectures. The source code will be available at https://github.com/KeyanHu-git/IDGBR.

SFNet: Fusion of Spatial and Frequency-Domain Features for Remote Sensing Image Forgery Detection

The rapid advancement of generative artificial intelligence is producing fake remote sensing imagery (RSI) that is increasingly difficult to detect, potentially leading to erroneous intelligence, fake news, and even conspiracy theories. Existing forgery detection methods typically rely on single visual features to capture predefined artifacts, such as spatial-domain cues to detect forged objects like roads or buildings in RSI, or frequency-domain features to identify artifacts from up-sampling operations in adversarial generative networks (GANs). However, the nature of artifacts can significantly differ depending on geographic terrain, land cover types, or specific features within the RSI. Moreover, these complex artifacts evolve as generative models become more sophisticated. In short, over-reliance on a single visual cue makes existing forgery detectors struggle to generalize across diverse remote sensing data. This paper proposed a novel forgery detection framework called SFNet, designed to identify fake images in diverse remote sensing data by leveraging spatial and frequency domain features. Specifically, to obtain rich and comprehensive visual information, SFNet employs two independent feature extractors to capture spatial and frequency domain features from input RSIs. To fully utilize the complementary domain features, the domain feature mapping module and the hybrid domain feature refinement module(CBAM attention) of SFNet are designed to successively align and fuse the multi-domain features while suppressing redundant information. Experiments on three datasets show that SFNet achieves an accuracy improvement of 4%-15.18% over the state-of-the-art RS forgery detection methods and exhibits robust generalization capabilities. The code is available at https://github.com/GeoX-Lab/RSTI/tree/main/SFNet.

Efficient Network Automatic Relevance Determination

We propose Network Automatic Relevance Determination (NARD), an extension of ARD for linearly probabilistic models, to simultaneously model sparse relationships between inputs $X \in \mathbb R^{d \times N}$ and outputs $Y \in \mathbb R^{m \times N}$, while capturing the correlation structure among the $Y$. NARD employs a matrix normal prior which contains a sparsity-inducing parameter to identify and discard irrelevant features, thereby promoting sparsity in the model. Algorithmically, it iteratively updates both the precision matrix and the relationship between $Y$ and the refined inputs. To mitigate the computational inefficiencies of the $\mathcal O(m^3 + d^3)$ cost per iteration, we introduce Sequential NARD, which evaluates features sequentially, and a Surrogate Function Method, leveraging an efficient approximation of the marginal likelihood and simplifying the calculation of determinant and inverse of an intermediate matrix. Combining the Sequential update with the Surrogate Function method further reduces computational costs. The computational complexity per iteration for these three methods is reduced to $\mathcal O(m^3+p^3)$, $\mathcal O(m^3 + d^2)$, $\mathcal O(m^3+p^2)$, respectively, where $p \ll d$ is the final number of features in the model. Our methods demonstrate significant improvements in computational efficiency with comparable performance on both synthetic and real-world datasets.

Fast on the Easy, Deep on the Hard: Efficient Reasoning via Powered Length Penalty

Large language models (LLMs) have demonstrated significant advancements in reasoning capabilities, performing well on various challenging benchmarks. Techniques like Chain-of-Thought prompting have been introduced to further improve reasoning. However, these approaches frequently generate longer outputs, which in turn increase computational latency. Although some methods use reinforcement learning to shorten reasoning, they often apply uniform penalties without considering the problem's complexity, leading to suboptimal outcomes. In this study, we seek to enhance the efficiency of LLM reasoning by promoting conciseness for simpler problems while preserving sufficient reasoning for more complex ones for accuracy, thus improving the model's overall performance. Specifically, we manage the model's reasoning efficiency by dividing the reward function and including a novel penalty for output length. Our approach has yielded impressive outcomes in benchmark evaluations across three datasets: GSM8K, MATH500, and AIME2024. For the comparatively simpler datasets GSM8K and MATH500, our method has effectively shortened output lengths while preserving or enhancing accuracy. On the more demanding AIME2024 dataset, our approach has resulted in improved accuracy.

ChromFound: Towards A Universal Foundation Model for Single-Cell Chromatin Accessibility Data

The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present \textbf{ChromFound}, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.

Ophora: A Large-Scale Data-Driven Text-Guided Ophthalmic Surgical Video Generation Model

In ophthalmic surgery, developing an AI system capable of interpreting surgical videos and predicting subsequent operations requires numerous ophthalmic surgical videos with high-quality annotations, which are difficult to collect due to privacy concerns and labor consumption. Text-guided video generation (T2V) emerges as a promising solution to overcome this issue by generating ophthalmic surgical videos based on surgeon instructions. In this paper, we present Ophora, a pioneering model that can generate ophthalmic surgical videos following natural language instructions. To construct Ophora, we first propose a Comprehensive Data Curation pipeline to convert narrative ophthalmic surgical videos into a large-scale, high-quality dataset comprising over 160K video-instruction pairs, Ophora-160K. Then, we propose a Progressive Video-Instruction Tuning scheme to transfer rich spatial-temporal knowledge from a T2V model pre-trained on natural video-text datasets for privacy-preserved ophthalmic surgical video generation based on Ophora-160K. Experiments on video quality evaluation via quantitative analysis and ophthalmologist feedback demonstrate that Ophora can generate realistic and reliable ophthalmic surgical videos based on surgeon instructions. We also validate the capability of Ophora for empowering downstream tasks of ophthalmic surgical workflow understanding. Code is available at https://github.com/mar-cry/Ophora.

Learning from Noisy Pseudo-labels for All-Weather Land Cover Mapping

Semantic segmentation of SAR images has garnered significant attention in remote sensing due to the immunity of SAR sensors to cloudy weather and light conditions. Nevertheless, SAR imagery lacks detailed information and is plagued by significant speckle noise, rendering the annotation or segmentation of SAR images a formidable task. Recent efforts have resorted to annotating paired optical-SAR images to generate pseudo-labels through the utilization of an optical image segmentation network. However, these pseudo-labels are laden with noise, leading to suboptimal performance in SAR image segmentation. In this study, we introduce a more precise method for generating pseudo-labels by incorporating semi-supervised learning alongside a novel image resolution alignment augmentation. Furthermore, we introduce a symmetric cross-entropy loss to mitigate the impact of noisy pseudo-labels. Additionally, a bag of training and testing tricks is utilized to generate better land-cover mapping results. Our experiments on the GRSS data fusion contest indicate the effectiveness of the proposed method, which achieves first place. The code is available at https://github.com/StuLiu/DFC2025Track1.git.

Fin-R1: A Large Language Model for Financial Reasoning through Reinforcement Learning

Reasoning large language models are rapidly evolving across various domains. However, their capabilities in handling complex financial tasks still require in-depth exploration. In this paper, we introduce Fin-R1, a reasoning large language model specifically designed for the financial sector. Fin-R1 is built using a two-stage architecture, leveraging a financial reasoning dataset distilled and processed based on DeepSeek-R1. Through supervised fine-tuning (SFT) and reinforcement learning (RL) training, it demonstrates performance close to DeepSeek-R1 with a parameter size of 7 billion across a range of financial reasoning tasks. It achieves the state-of-the-art (SOTA) in the FinQA and ConvFinQA tasks between those LLMs in our evaluation, surpassing larger models in other tasks as well. Fin-R1 showcases strong reasoning and decision-making capabilities, providing solutions to various problems encountered in the financial domain. Our code is available at https://github.com/SUFE-AIFLM-Lab/Fin-R1.