Jiaxin Han

Anqi Li, Feng Li, Jiaxin Han et al.

Learned image compression (LIC) methods have experienced significant progress during recent years. However, these methods are primarily dedicated to optimizing the rate-distortion (R-D) performance at medium and high bitrates (> 0.1 bits per pixel (bpp)), while research on extremely low bitrates is limited. Besides, existing methods fail to explicitly explore the image structure and texture components crucial for image compression, treating them equally alongside uninformative components in networks. This can cause severe perceptual quality degradation, especially under low-bitrate scenarios. In this work, inspired by the success of pre-trained masked autoencoders (MAE) in many downstream tasks, we propose to rethink its mask sampling strategy from structure and texture perspectives for high redundancy reduction and discriminative feature representation, further unleashing the potential of LIC methods. Therefore, we present a dual-adaptive masking approach (DA-Mask) that samples visible patches based on the structure and texture distributions of original images. We combine DA-Mask and pre-trained MAE in masked image modeling (MIM) as an initial compressor that abstracts informative semantic context and texture representations. Such a pipeline can well cooperate with LIC networks to achieve further secondary compression while preserving promising reconstruction quality. Consequently, we propose a simple yet effective masked compression model (MCM), the first framework that unifies MIM and LIC end-to-end for extremely low-bitrate image compression. Extensive experiments have demonstrated that our approach outperforms recent state-of-the-art methods in R-D performance, visual quality, and downstream applications, at very low bitrates. Our code is available at https://github.com/lianqi1008/MCM.git.

Yi Fang, Haoran Xu, Jiaxin Han et al.

Foundation models have revolutionized various fields such as natural language processing (NLP) and computer vision (CV). While efforts have been made to transfer the success of the foundation models in general AI domains to biology, existing works focus on directly adopting the existing foundation model architectures from general machine learning domains without a systematic design considering the unique physicochemical and structural properties of each biological data modality. This leads to suboptimal performance, as these repurposed architectures struggle to capture the long-range dependencies, sparse information, and complex underlying ``grammars'' inherent to biological data. To address this gap, we introduce BioArc, a novel framework designed to move beyond intuition-driven architecture design towards principled, automated architecture discovery for biological foundation models. Leveraging Neural Architecture Search (NAS), BioArc systematically explores a vast architecture design space, evaluating architectures across multiple biological modalities while rigorously analyzing the interplay between architecture, tokenization, and training strategies. This large-scale analysis identifies novel, high-performance architectures, allowing us to distill a set of empirical design principles to guide future model development. Furthermore, to make the best of this set of discovered principled architectures, we propose and compare several architecture prediction methods that effectively and efficiently predict optimal architectures for new biological tasks. Overall, our work provides a foundational resource and a principled methodology to guide the creation of the next generation of task-specific and foundation models for biology.