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Opponent Shaping for Antibody Development

arXiv.org Artificial Intelligence

Anti-viral therapies are typically designed or evolved towards the current strains of a virus. In learning terms, this corresponds to a myopic best response, i.e., not considering the possible adaptive moves of the opponent. However, therapy-induced selective pressures act on viral antigens to drive the emergence of mutated strains, against which initial therapies have reduced efficacy. To motivate our work, we consider antibody designs that target not only the current viral strains but also the wide range of possible future variants that the virus might evolve into under the evolutionary pressure exerted by said antibodies. Building on a computational model of binding between antibodies and viral antigens (the Absolut! framework), we design and implement a genetic simulation of the viral evolutionary escape. Crucially, this allows our antibody optimisation algorithm to consider and influence the entire escape curve of the virus, i.e. to guide (or ''shape'') the viral evolution. This is inspired by opponent shaping which, in general-sum learning, accounts for the adaptation of the co-player rather than playing a myopic best response. Hence we call the optimised antibodies shapers. Within our simulations, we demonstrate that our shapers target both current and simulated future viral variants, outperforming the antibodies chosen in a myopic way. Furthermore, we show that shapers exert specific evolutionary pressure on the virus compared to myopic antibodies. Altogether, shapers modify the evolutionary trajectories of viral strains and minimise the viral escape compared to their myopic counterparts. While this is a simple model, we hope that our proposed paradigm will enable the discovery of better long-lived vaccines and antibody therapies in the future, enabled by rapid advancements in the capabilities of simulation tools.


Stable Online and Offline Reinforcement Learning for Antibody CDRH3 Design

arXiv.org Artificial Intelligence

The field of antibody-based therapeutics has grown significantly in recent years, with targeted antibodies emerging as a potentially effective approach to personalized therapies. Such therapies could be particularly beneficial for complex, highly individual diseases such as cancer. However, progress in this field is often constrained by the extensive search space of amino acid sequences that form the foundation of antibody design. In this study, we introduce a novel reinforcement learning method specifically tailored to address the unique challenges of this domain. We demonstrate that our method can learn the design of high-affinity antibodies against multiple targets in silico, utilizing either online interaction or offline datasets. To the best of our knowledge, our approach is the first of its kind and outperforms existing methods on all tested antigens in the Absolut!


Facebook Messenger boss says chatbots got 'really overhyped,' announces new native payment feature

#artificialintelligence

Facebook's chatbot platform had too much hype. That's what David Marcus, head of Facebook Messenger, said on stage today at TechCrunch Disrupt in San Francisco. Facebook first released its chatbot platform in April, enabling developers to build robots that use artificial intelligence and natural language processing to let people talk with businesses just like they do with friends and family on Messenger. At the April launch, Facebook showed how a commerce company like 1-800-FLOWERS could use chatbots to help people order flowers and automate communication with customers, for example. But after TechCrunch reporter Josh Constine noted today that the product was "half-baked" when it first launched and asked what was missing, Marcus said that expectations for chatbots were a bit overdone.