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Ben Raphael

Publications and source records attributed to Ben Raphael.

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Transport Clustering: Solving Low-Rank Optimal Transport via Clustering

Optimal transport (OT) finds a least cost transport plan between two probability distributions using a cost matrix defined on pairs of points. Unlike standard OT, which infers unstructured pointwise mappings, low-rank optimal transport explicitly constrains the rank of the transport plan to infer latent structure. This improves statistical stability and robustness, yields sharper parametric rates for estimating Wasserstein distances adaptive to the intrinsic rank, and generalizes $K$-means to co-clustering. These advantages, however, come at the cost of a non-convex and NP-hard optimization problem. We introduce transport clustering, an algorithm to compute a low-rank OT plan that reduces low-rank OT to a clustering problem on correspondences obtained from a full-rank $\textit{transport registration}$ step. We prove that this reduction yields polynomial-time, constant-factor approximation algorithms for low-rank OT: specifically, a $(1+\gamma)$ approximation for negative-type metrics and a $(1+\gamma+\sqrt{2\gamma}\,)$ approximation for kernel costs, where $\gamma \in [0,1]$ denotes the approximation ratio of the optimal full-rank solution relative to the low-rank optimal. Empirically, transport clustering outperforms existing low-rank OT solvers on synthetic benchmarks and large-scale, high-dimensional datasets.

cs.LG

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