Jiahao Kuang

Wei Du, Nuowei Liu, Jie Wang et al.

Language models trained with a fixed vocabulary struggle to generalize to novel or out-of-vocabulary words, limiting their flexibility in handling diverse token combinations. Existing dynamic vocabulary approaches attempt to address this limitation but face challenges such as fragmented codebases, lack of support for modern LLMs, and limited inference scalability. To overcome these issues, we introduce DVAGen, a fully open-source, unified framework designed for training, evaluation, and visualization of dynamic vocabulary-augmented language models. Our framework modularizes the pipeline for ease of customization, integrates seamlessly with open-source LLMs, and is the first to provide both CLI and WebUI tools for real-time result inspection. We validate the effectiveness of dynamic vocabulary methods on modern LLMs and demonstrate support for batch inference, significantly improving inference throughput.

Nuowei Liu, Jiahao Kuang, Yanting Liu et al.

Protein design is a fundamental challenge in biotechnology, aiming to design novel sequences with specific functions within the vast space of possible proteins. Recent advances in deep generative models have enabled function-based protein design from textual descriptions, yet struggle with structural plausibility. Inspired by classical protein design methods that leverage natural protein structures, we explore whether incorporating fragments from natural proteins can enhance foldability in generative models. Our empirical results show that even random incorporation of fragments improves foldability. Building on this insight, we introduce ProDVa, a novel protein design approach that integrates a text encoder for functional descriptions, a protein language model for designing proteins, and a fragment encoder to dynamically retrieve protein fragments based on textual functional descriptions. Experimental results demonstrate that our approach effectively designs protein sequences that are both functionally aligned and structurally plausible. Compared to state-of-the-art models, ProDVa achieves comparable function alignment using less than 0.04% of the training data, while designing significantly more well-folded proteins, with the proportion of proteins having pLDDT above 70 increasing by 7.38% and those with PAE below 10 increasing by 9.6%.

Jiahao Kuang, Nuowei Liu, Jie Wang et al.

Function-guided protein design is a crucial task with significant applications in drug discovery and enzyme engineering. However, the field lacks a unified and comprehensive evaluation framework. Current models are assessed using inconsistent and limited subsets of metrics, which prevents fair comparison and a clear understanding of the relationships between different evaluation criteria. To address this gap, we introduce PDFBench, the first comprehensive benchmark for function-guided denovo protein design. Our benchmark systematically evaluates eight state-of-the-art models on 16 metrics across two key settings: description-guided design, for which we repurpose the Mol-Instructions dataset, originally lacking quantitative benchmarking, and keyword-guided design, for which we introduce a new test set, SwissTest, created with a strict datetime cutoff to ensure data integrity. By benchmarking across a wide array of metrics and analyzing their correlations, PDFBench enables more reliable model comparisons and provides key insights to guide future research.