Siyu Long

Kangjie Zheng, Siyu Long, Tianyu Lu et al.

Protein language models have demonstrated significant potential in the field of protein engineering. However, current protein language models primarily operate at the residue scale, which limits their ability to provide information at the atom level. This limitation prevents us from fully exploiting the capabilities of protein language models for applications involving both proteins and small molecules. In this paper, we propose ESM-AA (ESM All-Atom), a novel approach that enables atom-scale and residue-scale unified molecular modeling. ESM-AA achieves this by pre-training on multi-scale code-switch protein sequences and utilizing a multi-scale position encoding to capture relationships among residues and atoms. Experimental results indicate that ESM-AA surpasses previous methods in protein-molecule tasks, demonstrating the full utilization of protein language models. Further investigations reveal that through unified molecular modeling, ESM-AA not only gains molecular knowledge but also retains its understanding of proteins. The source codes of ESM-AA are publicly released at https://github.com/zhengkangjie/ESM-AA.

Changze Lv, Jiang Zhou, Siyu Long et al.

We introduce AMix-1, a powerful protein foundation model built on Bayesian Flow Networks and empowered by a systematic training methodology, encompassing pretraining scaling laws, emergent capability analysis, in-context learning mechanism, and test-time scaling algorithm. To guarantee robust scalability, we establish a predictive scaling law and reveal the progressive emergence of structural understanding via loss perspective, culminating in a strong 1.7-billion model. Building on this foundation, we devise a multiple sequence alignment (MSA)-based in-context learning strategy to unify protein design into a general framework, where AMix-1 recognizes deep evolutionary signals among MSAs and consistently generates structurally and functionally coherent proteins. This framework enables the successful design of a dramatically improved AmeR variant with an up to $50\times$ activity increase over its wild type. Pushing the boundaries of protein engineering, we further empower AMix-1 with an evolutionary test-time scaling algorithm for in silico directed evolution that delivers substantial, scalable performance gains as verification budgets are intensified, laying the groundwork for next-generation lab-in-the-loop protein design.

Nantao Zheng, Siyu Long, Xinyu Dai

Canonical relation extraction aims to extract relational triples from sentences, where the triple elements (entity pairs and their relationship) are mapped to the knowledge base. Recently, methods based on the encoder-decoder architecture are proposed and achieve promising results. However, these methods cannot well utilize the entity information, which is merely used as augmented training data. Moreover, they are incapable of representing novel entities, since no embeddings have been learned for them. In this paper, we propose a novel framework, Bi-Encoder-Decoder (BED), to solve the above issues. Specifically, to fully utilize entity information, we employ an encoder to encode semantics of this information, leading to high-quality entity representations. For novel entities, given a trained entity encoder, their representations can be easily generated. Experimental results on two datasets show that, our method achieves a significant performance improvement over the previous state-of-the-art and handle novel entities well without retraining.

Siyu Long, Ran Wang, Kun Tao et al.

Machine reading comprehension (MRC) is the task that asks a machine to answer questions based on a given context. For Chinese MRC, due to the non-literal and non-compositional semantic characteristics, Chinese idioms pose unique challenges for machines to understand. Previous studies tend to treat idioms separately without fully exploiting the relationship among them. In this paper, we first define the concept of literal meaning coverage to measure the consistency between semantics and literal meanings for Chinese idioms. With the definition, we prove that the literal meanings of many idioms are far from their semantics, and we also verify that the synonymic relationship can mitigate this inconsistency, which would be beneficial for idiom comprehension. Furthermore, to fully utilize the synonymic relationship, we propose the synonym knowledge enhanced reader. Specifically, for each idiom, we first construct a synonym graph according to the annotations from a high-quality synonym dictionary or the cosine similarity between the pre-trained idiom embeddings and then incorporate the graph attention network and gate mechanism to encode the graph. Experimental results on ChID, a large-scale Chinese idiom reading comprehension dataset, show that our model achieves state-of-the-art performance.