Diffusion Model with Representation Alignment for Protein Inverse Folding

Protein inverse folding is a fundamental problem in bioinformatics, aiming to recover the amino acid sequences from a given protein backbone structure. Despite the success of existing methods, they struggle to fully capture the intricate inter-residue relationships critical for accurate sequence prediction. We propose a novel method that leverages diffusion models with representation alignment (DMRA), which enhances diffusion-based inverse folding by (1) proposing a shared center that aggregates contextual information from the entire protein structure and selectively distributes it to each residue; and (2) aligning noisy hidden representations with clean semantic representations during the denoising process. This is achieved by predefined semantic representations for amino acid types and a representation alignment method that utilizes type embeddings as semantic feedback to normalize each residue. In experiments, we conduct extensive evaluations on the CATH4.2 dataset to demonstrate that DMRA outperforms leading methods, achieving state-of-the-art performance and exhibiting strong generalization capabilities on the TS50 and TS500 datasets.

Dynamic-LLaVA: Efficient Multimodal Large Language Models via Dynamic Vision-language Context Sparsification

Multimodal Large Language Models (MLLMs) have achieved remarkable success in vision understanding, reasoning, and interaction. However, the inference computation and memory increase progressively with the generation of output tokens during decoding, directly affecting the efficacy of MLLMs. Existing methods attempt to reduce the vision context redundancy to achieve efficient MLLMs. Unfortunately, the efficiency benefits of the vision context reduction in the prefill stage gradually diminish during the decoding stage. To address this problem, we proposed a dynamic vision-language context sparsification framework Dynamic-LLaVA, which dynamically reduces the redundancy of vision context in the prefill stage and decreases the memory and computation overhead of the generated language context during decoding. Dynamic-LLaVA designs a tailored sparsification inference scheme for different inference modes, i.e., prefill, decoding with and without KV cache, to achieve efficient inference of MLLMs. In practice, Dynamic-LLaVA can reduce computation consumption by $\sim$75\% in the prefill stage. Meanwhile, throughout the entire generation process of MLLMs, Dynamic-LLaVA reduces the $\sim$50\% computation consumption under decoding without KV cache, while saving $\sim$50\% GPU memory overhead when decoding with KV cache, due to the vision-language context sparsification. Extensive experiments also demonstrate that Dynamic-LLaVA achieves efficient inference for MLLMs with negligible understanding and generation ability degradation or even performance gains compared to the full-context inference baselines. Code is available at https://github.com/Osilly/dynamic_llava .