arXiv subjects

Ellen Zhong

Publications and source records attributed to Ellen Zhong.

3 recordsLinked to original sources

arXiv2025

Generative AI for Biosciences: Emerging Threats and Roadmap to Biosecurity

The rapid adoption of generative artificial intelligence (GenAI) in the biosciences is transforming biotechnology, medicine, and synthetic biology. Yet this advancement is intrinsically linked to new vulnerabilities, as GenAI lowers the barrier to misuse and introduces novel biosecurity threats, such as generating synthetic viral proteins or toxins. These dual-use risks are often overlooked, as existing safety guardrails remain fragile and can be circumvented through deceptive prompts or jailbreak techniques. In this Perspective, we first outline the current state of GenAI in the biosciences and emerging threat vectors ranging from jailbreak attacks and privacy risks to the dual-use challenges posed by autonomous AI agents. We then examine urgent gaps in regulation and oversight, drawing on insights from 130 expert interviews across academia, government, industry, and policy. A large majority ($\approx 76$\%) expressed concern over AI misuse in biology, and 74\% called for the development of new governance frameworks. Finally, we explore technical pathways to mitigation, advocating a multi-layered approach to GenAI safety. These defenses include rigorous data filtering, alignment with ethical principles during development, and real-time monitoring to block harmful requests. Together, these strategies provide a blueprint for embedding security throughout the GenAI lifecycle. As GenAI becomes integrated into the biosciences, safeguarding this frontier requires an immediate commitment to both adaptive governance and secure-by-design technologies.

cs.CR↗

arXiv2022

Latent Space Diffusion Models of Cryo-EM Structures

Cryo-electron microscopy (cryo-EM) is unique among tools in structural biology in its ability to image large, dynamic protein complexes. Key to this ability is image processing algorithms for heterogeneous cryo-EM reconstruction, including recent deep learning-based approaches. The state-of-the-art method cryoDRGN uses a Variational Autoencoder (VAE) framework to learn a continuous distribution of protein structures from single particle cryo-EM imaging data. While cryoDRGN can model complex structural motions, the Gaussian prior distribution of the VAE fails to match the aggregate approximate posterior, which prevents generative sampling of structures especially for multi-modal distributions (e.g. compositional heterogeneity). Here, we train a diffusion model as an expressive, learnable prior in the cryoDRGN framework. Our approach learns a high-quality generative model over molecular conformations directly from cryo-EM imaging data. We show the ability to sample from the model on two synthetic and two real datasets, where samples accurately follow the data distribution unlike samples from the VAE prior distribution. We also demonstrate how the diffusion model prior can be leveraged for fast latent space traversal and interpolation between states of interest. By learning an accurate model of the data distribution, our method unlocks tools in generative modeling, sampling, and distribution analysis for heterogeneous cryo-EM ensembles.

q-bio.QM↗

arXiv2022

Deep Generative Modeling for Volume Reconstruction in Cryo-Electron Microscopy

Recent breakthroughs in high-resolution imaging of biomolecules in solution with cryo-electron microscopy (cryo-EM) have unlocked new doors for the reconstruction of molecular volumes, thereby promising further advances in biology, chemistry, and pharmacological research. Recent next-generation volume reconstruction algorithms that combine generative modeling with end-to-end unsupervised deep learning techniques have shown promising preliminary results, but still face considerable technical and theoretical hurdles when applied to experimental cryo-EM images. In light of the proliferation of such methods, we propose here a critical review of recent advances in the field of deep generative modeling for cryo-EM volume reconstruction. The present review aims to (i) unify and compare these new methods using a consistent statistical framework, (ii) present them using a terminology familiar to machine learning researchers and computational biologists with no specific background in cryo-EM, and (iii) provide the necessary perspective on current advances to highlight their relative strengths and weaknesses, along with outstanding bottlenecks and avenues for improvements in the field. This review might also raise the interest of computer vision practitioners, as it highlights significant limits of deep generative models in low signal-to-noise regimes -- therefore emphasizing a need for new theoretical and methodological developments.

eess.IV↗