CD-TVD: Contrastive Diffusion for 3D Super-Resolution with Scarce High-Resolution Time-Varying Data

Large-scale scientific simulations require significant resources to generate high-resolution time-varying data (TVD). While super-resolution is an efficient post-processing strategy to reduce costs, existing methods rely on a large amount of HR training data, limiting their applicability to diverse simulation scenarios. To address this constraint, we proposed CD-TVD, a novel framework that combines contrastive learning and an improved diffusion-based super-resolution model to achieve accurate 3D super-resolution from limited time-step high-resolution data. During pre-training on historical simulation data, the contrastive encoder and diffusion superresolution modules learn degradation patterns and detailed features of high-resolution and low-resolution samples. In the training phase, the improved diffusion model with a local attention mechanism is fine-tuned using only one newly generated high-resolution timestep, leveraging the degradation knowledge learned by the encoder. This design minimizes the reliance on large-scale high-resolution datasets while maintaining the capability to recover fine-grained details. Experimental results on fluid and atmospheric simulation datasets confirm that CD-TVD delivers accurate and resource-efficient 3D super-resolution, marking a significant advancement in data augmentation for large-scale scientific simulations. The code is available at https://github.com/Xin-Gao-private/CD-TVD.

EcoTransformer: Attention without Multiplication

The Transformer, with its scaled dot-product attention mechanism, has become a foundational architecture in modern AI. However, this mechanism is computationally intensive and incurs substantial energy costs. We propose a new Transformer architecture EcoTransformer, in which the output context vector is constructed as the convolution of the values using a Laplacian kernel, where the distances are measured by the L1 metric between the queries and keys. Compared to dot-product based attention, the new attention score calculation is free of matrix multiplication. It performs on par with, or even surpasses, scaled dot-product attention in NLP, bioinformatics, and vision tasks, while consuming significantly less energy.

LRMR: LLM-Driven Relational Multi-node Ranking for Lymph Node Metastasis Assessment in Rectal Cancer

Accurate preoperative assessment of lymph node (LN) metastasis in rectal cancer guides treatment decisions, yet conventional MRI evaluation based on morphological criteria shows limited diagnostic performance. While some artificial intelligence models have been developed, they often operate as black boxes, lacking the interpretability needed for clinical trust. Moreover, these models typically evaluate nodes in isolation, overlooking the patient-level context. To address these limitations, we introduce LRMR, an LLM-Driven Relational Multi-node Ranking framework. This approach reframes the diagnostic task from a direct classification problem into a structured reasoning and ranking process. The LRMR framework operates in two stages. First, a multimodal large language model (LLM) analyzes a composite montage image of all LNs from a patient, generating a structured report that details ten distinct radiological features. Second, a text-based LLM performs pairwise comparisons of these reports between different patients, establishing a relative risk ranking based on the severity and number of adverse features. We evaluated our method on a retrospective cohort of 117 rectal cancer patients. LRMR achieved an area under the curve (AUC) of 0.7917 and an F1-score of 0.7200, outperforming a range of deep learning baselines, including ResNet50 (AUC 0.7708). Ablation studies confirmed the value of our two main contributions: removing the relational ranking stage or the structured prompting stage led to a significant performance drop, with AUCs falling to 0.6875 and 0.6458, respectively. Our work demonstrates that decoupling visual perception from cognitive reasoning through a two-stage LLM framework offers a powerful, interpretable, and effective new paradigm for assessing lymph node metastasis in rectal cancer.

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.

CFP-Gen: Combinatorial Functional Protein Generation via Diffusion Language Models

Existing PLMs generate protein sequences based on a single-condition constraint from a specific modality, struggling to simultaneously satisfy multiple constraints across different modalities. In this work, we introduce CFP-Gen, a novel diffusion language model for Combinatorial Functional Protein GENeration. CFP-Gen facilitates the de novo protein design by integrating multimodal conditions with functional, sequence, and structural constraints. Specifically, an Annotation-Guided Feature Modulation (AGFM) module is introduced to dynamically adjust the protein feature distribution based on composable functional annotations, e.g., GO terms, IPR domains and EC numbers. Meanwhile, the Residue-Controlled Functional Encoding (RCFE) module captures residue-wise interaction to ensure more precise control. Additionally, off-the-shelf 3D structure encoders can be seamlessly integrated to impose geometric constraints. We demonstrate that CFP-Gen enables high-throughput generation of novel proteins with functionality comparable to natural proteins, while achieving a high success rate in designing multifunctional proteins. Code and data available at https://github.com/yinjunbo/cfpgen.

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.

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.

WeGA: Weakly-Supervised Global-Local Affinity Learning Framework for Lymph Node Metastasis Prediction in Rectal Cancer

Accurate lymph node metastasis (LNM) assessment in rectal cancer is essential for treatment planning, yet current MRI-based evaluation shows unsatisfactory accuracy, leading to suboptimal clinical decisions. Developing automated systems also faces significant obstacles, primarily the lack of node-level annotations. Previous methods treat lymph nodes as isolated entities rather than as an interconnected system, overlooking valuable spatial and contextual information. To solve this problem, we present WeGA, a novel weakly-supervised global-local affinity learning framework that addresses these challenges through three key innovations: 1) a dual-branch architecture with DINOv2 backbone for global context and residual encoder for local node details; 2) a global-local affinity extractor that aligns features across scales through cross-attention fusion; and 3) a regional affinity loss that enforces structural coherence between classification maps and anatomical regions. Experiments across one internal and two external test centers demonstrate that WeGA outperforms existing methods, achieving AUCs of 0.750, 0.822, and 0.802 respectively. By effectively modeling the relationships between individual lymph nodes and their collective context, WeGA provides a more accurate and generalizable approach for lymph node metastasis prediction, potentially enhancing diagnostic precision and treatment selection for rectal cancer patients.

ABS-Mamba: SAM2-Driven Bidirectional Spiral Mamba Network for Medical Image Translation

Accurate multi-modal medical image translation requires ha-rmonizing global anatomical semantics and local structural fidelity, a challenge complicated by intermodality information loss and structural distortion. We propose ABS-Mamba, a novel architecture integrating the Segment Anything Model 2 (SAM2) for organ-aware semantic representation, specialized convolutional neural networks (CNNs) for preserving modality-specific edge and texture details, and Mamba's selective state-space modeling for efficient long- and short-range feature dependencies. Structurally, our dual-resolution framework leverages SAM2's image encoder to capture organ-scale semantics from high-resolution inputs, while a parallel CNNs branch extracts fine-grained local features. The Robust Feature Fusion Network (RFFN) integrates these epresentations, and the Bidirectional Mamba Residual Network (BMRN) models spatial dependencies using spiral scanning and bidirectional state-space dynamics. A three-stage skip fusion decoder enhances edge and texture fidelity. We employ Efficient Low-Rank Adaptation (LoRA+) fine-tuning to enable precise domain specialization while maintaining the foundational capabilities of the pre-trained components. Extensive experimental validation on the SynthRAD2023 and BraTS2019 datasets demonstrates that ABS-Mamba outperforms state-of-the-art methods, delivering high-fidelity cross-modal synthesis that preserves anatomical semantics and structural details to enhance diagnostic accuracy in clinical applications. The code is available at https://github.com/gatina-yone/ABS-Mamba

Harmonizing Intra-coherence and Inter-divergence in Ensemble Attacks for Adversarial Transferability

The development of model ensemble attacks has significantly improved the transferability of adversarial examples, but this progress also poses severe threats to the security of deep neural networks. Existing methods, however, face two critical challenges: insufficient capture of shared gradient directions across models and a lack of adaptive weight allocation mechanisms. To address these issues, we propose a novel method Harmonized Ensemble for Adversarial Transferability (HEAT), which introduces domain generalization into adversarial example generation for the first time. HEAT consists of two key modules: Consensus Gradient Direction Synthesizer, which uses Singular Value Decomposition to synthesize shared gradient directions; and Dual-Harmony Weight Orchestrator which dynamically balances intra-domain coherence, stabilizing gradients within individual models, and inter-domain diversity, enhancing transferability across models. Experimental results demonstrate that HEAT significantly outperforms existing methods across various datasets and settings, offering a new perspective and direction for adversarial attack research.