Bayesian Optimization of Antibodies Informed by a Generative Model of Evolving Sequences

To build effective therapeutics, biologists iteratively mutate antibody sequences to improve binding and stability. Proposed mutations can be informed by previous measurements or by learning from large antibody databases to predict only typical antibodies. Unfortunately, the space of typical antibodies is enormous to search, and experiments often fail to find suitable antibodies on a budget. We introduce Clone-informed Bayesian Optimization (CloneBO), a Bayesian optimization procedure that efficiently optimizes antibodies in the lab by teaching a generative model how our immune system optimizes antibodies. Our immune system makes antibodies by iteratively evolving specific portions of their sequences to bind their target strongly and stably, resulting in a set of related, evolving sequences known as a clonal family. We train a large language model, CloneLM, on hundreds of thousands of clonal families and use it to design sequences with mutations that are most likely to optimize an antibody within the human immune system. We propose to guide our designs to fit previous measurements with a twisted sequential Monte Carlo procedure. We show that CloneBO optimizes antibodies substantially more efficiently than previous methods in realistic in silico experiments and designs stronger and more stable binders in in vitro wet lab experiments.

A Multi-Modal Method for Satire Detection using Textual and Visual Cues

Satire is a form of humorous critique, but it is sometimes misinterpreted by readers as legitimate news, which can lead to harmful consequences. We observe that the images used in satirical news articles often contain absurd or ridiculous content and that image manipulation is used to create fictional scenarios. While previous work have studied text-based methods, in this work we propose a multi-modal approach based on state-of-the-art visiolinguistic model ViLBERT. To this end, we create a new dataset consisting of images and headlines of regular and satirical news for the task of satire detection. We fine-tune ViLBERT on the dataset and train a convolutional neural network that uses an image forensics technique. Evaluation on the dataset shows that our proposed multi-modal approach outperforms image-only, text-only, and simple fusion baselines.