Tianyu Lu

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.

Weidi Luo, Tianyu Lu, Qiming Zhang et al.

Recent advances in multi-modal large reasoning models (MLRMs) have shown significant ability to interpret complex visual content. While these models enable impressive reasoning capabilities, they also introduce novel and underexplored privacy risks. In this paper, we identify a novel category of privacy leakage in MLRMs: Adversaries can infer sensitive geolocation information, such as a user's home address or neighborhood, from user-generated images, including selfies captured in private settings. To formalize and evaluate these risks, we propose a three-level visual privacy risk framework that categorizes image content based on contextual sensitivity and potential for location inference. We further introduce DoxBench, a curated dataset of 500 real-world images reflecting diverse privacy scenarios. Our evaluation across 11 advanced MLRMs and MLLMs demonstrates that these models consistently outperform non-expert humans in geolocation inference and can effectively leak location-related private information. This significantly lowers the barrier for adversaries to obtain users' sensitive geolocation information. We further analyze and identify two primary factors contributing to this vulnerability: (1) MLRMs exhibit strong reasoning capabilities by leveraging visual clues in combination with their internal world knowledge; and (2) MLRMs frequently rely on privacy-related visual clues for inference without any built-in mechanisms to suppress or avoid such usage. To better understand and demonstrate real-world attack feasibility, we propose GeoMiner, a collaborative attack framework that decomposes the prediction process into two stages: clue extraction and reasoning to improve geolocation performance while introducing a novel attack perspective. Our findings highlight the urgent need to reassess inference-time privacy risks in MLRMs to better protect users' sensitive information.

Tianyu Lu, Alex X. Lu, Alan M. Moses

Large self-supervised models pretrained on millions of protein sequences have recently gained popularity in generating embeddings of protein sequences for protein function prediction. However, the absence of random baselines makes it difficult to conclude whether pretraining has learned useful information for protein function prediction. Here we show that one-hot encoding and random embeddings, both of which do not require any pretraining, are strong baselines for protein function prediction across 14 diverse sequence-to-function tasks.