AF2-Mutation: Adversarial Sequence Mutations against AlphaFold2 on Protein Tertiary Structure Prediction

Deep learning-based approaches, such as AlphaFold2 (AF2), have significantly advanced protein tertiary structure prediction, achieving results comparable to real biological experimental methods. While AF2 has shown limitations in predicting the effects of mutations, its robustness against sequence mutations remains to be determined. Starting with the wild-type (WT) sequence, we investigate adversarial sequences generated via an evolutionary approach, which AF2 predicts to be substantially different from WT. Our experiments on CASP14 reveal that by modifying merely three residues in the protein sequence using a combination of replacement, deletion, and insertion strategies, the alteration in AF2's predictions, as measured by the Local Distance Difference Test (lDDT), reaches 46.61. Moreover, when applied to a specific protein, SPNS2, our proposed algorithm successfully identifies biologically meaningful residues critical to protein structure determination and potentially indicates alternative conformations, thus significantly expediting the experimental process.

Cross-Domain Few-Shot Relation Extraction via Representation Learning and Domain Adaptation

Cross-domain few-shot relation extraction poses a great challenge for the existing few-shot learning methods and domain adaptation methods when the source domain and target domain have large discrepancies. This paper proposes a method by combining the idea of few-shot learning and domain adaptation to deal with this problem. In the proposed method, an encoder, learned by optimizing a representation loss and an adversarial loss, is used to extract the relation of sentences in the source and target domain. The representation loss, including a cross-entropy loss and a contrastive loss, makes the encoder extract the relation of the source domain and keep the geometric structure of the classes in the source domain. And the adversarial loss is used to merge the source domain and target domain. The experimental results on the benchmark FewRel dataset demonstrate that the proposed method can outperform some state-of-the-art methods.