Daily Papers

We propose the first unified adversarial attack benchmark for Genomic Foundation Models (GFMs), named GenoArmory. Unlike existing GFM benchmarks, GenoArmory offers the first comprehensive evaluation framework to systematically assess the vulnerability of GFMs to adversarial attacks. Methodologically, we evaluate the adversarial robustness of five state-of-the-art GFMs using four widely adopted attack algorithms and three defense strategies. Importantly, our benchmark provides an accessible and comprehensive framework to analyze GFM vulnerabilities with respect to model architecture, quantization schemes, and training datasets. Additionally, we introduce GenoAdv, a new adversarial sample dataset designed to improve GFM safety. Empirically, classification models exhibit greater robustness to adversarial perturbations compared to generative models, highlighting the impact of task type on model vulnerability. Moreover, adversarial attacks frequently target biologically significant genomic regions, suggesting that these models effectively capture meaningful sequence features.

We propose the first unified adversarial attack benchmark for Genomic Foundation Models (GFMs), named GERM. Unlike existing GFM benchmarks, GERM offers the first comprehensive evaluation framework to systematically assess the vulnerability of GFMs to adversarial attacks. Methodologically, we evaluate the adversarial robustness of five state-of-the-art GFMs using four widely adopted attack algorithms and three defense strategies. Importantly, our benchmark provides an accessible and comprehensive framework to analyze GFM vulnerabilities with respect to model architecture, quantization schemes, and training datasets. Empirically, transformer-based models exhibit greater robustness to adversarial perturbations compared to HyenaDNA, highlighting the impact of architectural design on vulnerability. Moreover, adversarial attacks frequently target biologically significant genomic regions, suggesting that these models effectively capture meaningful sequence features.

Geospatial raster data, such as that collected by satellite-based imaging systems at different times and spectral bands, hold immense potential for enabling a wide range of high-impact applications. This potential stems from the rich information that is spatially and temporally contextualized across multiple channels and sensing modalities. Recent work has adapted existing self-supervised learning approaches for such geospatial data. However, they fall short of scalable model architectures, leading to inflexibility and computational inefficiencies when faced with an increasing number of channels and modalities. To address these limitations, we introduce Low-rank Efficient Spatial-Spectral Vision Transformer with three key innovations: i) the LESS Attention Block that approximates high-dimensional spatial-spectral attention through Kronecker's product of the low-dimensional spatial and spectral attention components; ii) the Continuous Positional-Channel Embedding Layer that preserves both the continuity and physical characteristics of each spatial-spectral patch; and iii) the Perception Field Mask that exploits local spatial dependencies by constraining attention to neighboring patches. To evaluate the proposed innovations, we construct GFM-Bench, which serves as a comprehensive benchmark for such geospatial raster data. We pretrain LESS ViT using a Hyperspectral Masked Autoencoder framework with integrated positional and channel masking strategies. Experimental results demonstrate that our proposed method achieves competitive performance against state-of-the-art multi-modal geospatial foundation models while outperforming them on cross-satellite generalization tasks with higher computational efficiency. The flexibility and extensibility of our framework make it a promising direction for future geospatial data analysis tasks that involve a wide range of modalities and channels.

The code of nature, embedded in DNA and RNA genomes since the origin of life, holds immense potential to impact both humans and ecosystems through genome modeling. Genomic Foundation Models (GFMs) have emerged as a transformative approach to decoding the genome. As GFMs scale up and reshape the landscape of AI-driven genomics, the field faces an urgent need for rigorous and reproducible evaluation. We present OmniGenBench, a modular benchmarking platform designed to unify the data, model, benchmarking, and interpretability layers across GFMs. OmniGenBench enables standardized, one-command evaluation of any GFM across five benchmark suites, with seamless integration of over 31 open-source models. Through automated pipelines and community-extensible features, the platform addresses critical reproducibility challenges, including data transparency, model interoperability, benchmark fragmentation, and black-box interpretability. OmniGenBench aims to serve as foundational infrastructure for reproducible genomic AI research, accelerating trustworthy discovery and collaborative innovation in the era of genome-scale modeling.

Research on geospatial foundation models (GFMs) has become a trending topic in geospatial artificial intelligence (AI) research due to their potential for achieving high generalizability and domain adaptability, reducing model training costs for individual researchers. Unlike large language models, such as ChatGPT, constructing visual foundation models for image analysis, particularly in remote sensing, encountered significant challenges such as formulating diverse vision tasks into a general problem framework. This paper evaluates the recently released NASA-IBM GFM Prithvi for its predictive performance on high-level image analysis tasks across multiple benchmark datasets. Prithvi was selected because it is one of the first open-source GFMs trained on time-series of high-resolution remote sensing imagery. A series of experiments were designed to assess Prithvi's performance as compared to other pre-trained task-specific AI models in geospatial image analysis. New strategies, including band adaptation, multi-scale feature generation, and fine-tuning techniques, are introduced and integrated into an image analysis pipeline to enhance Prithvi's domain adaptation capability and improve model performance. In-depth analyses reveal Prithvi's strengths and weaknesses, offering insights for both improving Prithvi and developing future visual foundation models for geospatial tasks.

Flow matching casts sample generation as learning a continuous-time velocity field that transports noise to data. Existing flow matching networks typically predict each point's velocity independently, considering only its location and time along its flow trajectory, and ignoring neighboring points. However, this pointwise approach may overlook correlations between points along the generation trajectory that could enhance velocity predictions, thereby improving downstream generation quality. To address this, we propose Graph Flow Matching (GFM), a lightweight enhancement that decomposes the learned velocity into a reaction term -- any standard flow matching network -- and a diffusion term that aggregates neighbor information via a graph neural module. This reaction-diffusion formulation retains the scalability of deep flow models while enriching velocity predictions with local context, all at minimal additional computational cost. Operating in the latent space of a pretrained variational autoencoder, GFM consistently improves Fr\'echet Inception Distance (FID) and recall across five image generation benchmarks (LSUN Church, LSUN Bedroom, FFHQ, AFHQ-Cat, and CelebA-HQ at 256times256), demonstrating its effectiveness as a modular enhancement to existing flow matching architectures.