DreamDA: Generative Data Augmentation with Diffusion Models

The acquisition of large-scale, high-quality data is a resource-intensive and time-consuming endeavor. Compared to conventional Data Augmentation (DA) techniques (e.g. cropping and rotation), exploiting prevailing diffusion models for data generation has received scant attention in classification tasks. Existing generative DA methods either inadequately bridge the domain gap between real-world and synthesized images, or inherently suffer from a lack of diversity. To solve these issues, this paper proposes a new classification-oriented framework DreamDA, which enables data synthesis and label generation by way of diffusion models. DreamDA generates diverse samples that adhere to the original data distribution by considering training images in the original data as seeds and perturbing their reverse diffusion process. In addition, since the labels of the generated data may not align with the labels of their corresponding seed images, we introduce a self-training paradigm for generating pseudo labels and training classifiers using the synthesized data. Extensive experiments across four tasks and five datasets demonstrate consistent improvements over strong baselines, revealing the efficacy of DreamDA in synthesizing high-quality and diverse images with accurate labels. Our code will be available at https://github.com/yunxiangfu2001/DreamDA.

Protein Representation Learning via Knowledge Enhanced Primary Structure Modeling

Protein representation learning has primarily benefited from the remarkable development of language models (LMs). Accordingly, pre-trained protein models also suffer from a problem in LMs: a lack of factual knowledge. The recent solution models the relationships between protein and associated knowledge terms as the knowledge encoding objective. However, it fails to explore the relationships at a more granular level, i.e., the token level. To mitigate this, we propose Knowledge-exploited Auto-encoder for Protein (KeAP), which performs token-level knowledge graph exploration for protein representation learning. In practice, non-masked amino acids iteratively query the associated knowledge tokens to extract and integrate helpful information for restoring masked amino acids via attention. We show that KeAP can consistently outperform the previous counterpart on 9 representative downstream applications, sometimes surpassing it by large margins. These results suggest that KeAP provides an alternative yet effective way to perform knowledge enhanced protein representation learning.