Antibodies are crucial proteins produced by the immune system to eliminate harmful foreign substances and have become pivotal therapeutic agents for treating human diseases.

Neural Information Processing Systems http://nips.cc/

Neural Information Processing Systems http://nips.cc/

Antibodies are crucial proteins produced by the immune system to eliminate harmful foreign substances and have become pivotal therapeutic agents for treating human diseases. To accelerate the discovery of antibody therapeutics, there is growing interest in constructing language models using antibody sequences. However, the applicability of pre-trained language models for antibody discovery has not been thoroughly evaluated due to the scarcity of labeled datasets. To overcome these limitations, we introduce AVIDa-SARS-CoV-2, a dataset featuring the antigen-variable domain of heavy chain of heavy chain antibody (VHH) interactions obtained from two alpacas immunized with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike proteins. AVIDa-SARS-CoV-2 includes binary labels indicating the binding or non-binding of diverse VHH sequences to 12 SARS-CoV-2 mutants, such as the Delta and Omicron variants. Furthermore, we release VHHCorpus-2M, a pre-training dataset for antibody language models, containing over two million VHH sequences. We report benchmark results for predicting SARS-CoV-2-VHH binding using VHHBERT pre-trained on VHHCorpus-2M and existing general protein and antibody-specific pre-trained language models. These results confirm that AVIDa-SARS-CoV-2 provides valuable benchmarks for evaluating the representation capabilities of antibody language models for binding prediction, thereby facilitating the development of AI-driven antibody discovery.

Visual question answering (VQA) is challenging not only because the model has to handle multi-modal information, but also because it is just so hard to collect sufficient training examples -- there are too many questions one can ask about an image. As a result, a VQA model trained solely on human-annotated examples could easily over-fit specific question styles or image contents that are being asked, leaving the model largely ignorant about the sheer diversity of questions. Existing methods address this issue primarily by introducing an auxiliary task such as visual grounding, cycle consistency, or debiasing. In this paper, we take a drastically different approach. We found that many of the "unknowns" to the learned VQA model are indeed "known" in the dataset implicitly. For instance, questions asking about the same object in different images are likely paraphrases; the number of detected or annotated objects in an image already provides the answer to the "how many" question, even if the question has not been annotated for that image. Building upon these insights, we present a simple data augmentation pipeline SimpleAug to turn this "known" knowledge into training examples for VQA. We show that these augmented examples can notably improve the learned VQA models' performance, not only on the VQA-CP dataset with language prior shifts but also on the VQA v2 dataset without such shifts. Our method further opens up the door to leverage weakly-labeled or unlabeled images in a principled way to enhance VQA models. Our code and data are publicly available at https://github.com/heendung/simpleAUG.