Haowen Xiao

Fukang Ge, Jiarui Zhu, Linjie Zhang et al.

Modern AI technologies for drug discovery are distributed across heterogeneous platforms-including web applications, desktop environments, and code libraries-leading to fragmented workflows, inconsistent interfaces, and high integration overhead. We present an agentic end-to-end drug design framework that leverages a Large Language Model (LLM) in conjunction with the Model Context Protocol (MCP) to dynamically coordinate access to biochemical databases, modular toolchains, and task-specific AI models. The system integrates four state-of-the-art components: MaSIF (MaSIF-site and MaSIF-seed-search) for geometric deep learning-based identification of protein-protein interaction (PPI) sites, Rosetta for grafting protein fragments onto protein backbones to form mini proteins, ProteinMPNN for amino acid sequences redesign, and AlphaFold3 for near-experimental accuracy in complex structure prediction. Starting from a target structure, the framework supports de novo binder generation via surface analysis, scaffold grafting and pose construction, sequence optimization, and structure prediction. Additionally, by replacing rigid, script-based workflows with a protocol-driven, LLM-coordinated architecture, the framework improves reproducibility, reduces manual overhead, and ensures extensibility, portability, and auditability across the entire drug design process.

Yutao Jin, Haowen Xiao, Junyong Zhai et al.

Mild Cognitive Impairment (MCI) serves as a prodromal stage of Alzheimer's Disease (AD), where early identification and intervention can effectively slow the progression to dementia. However, diagnosing AD remains a significant challenge in neurology due to the confounders caused mainly by the selection bias of multi-modal data and the complex relationships between variables. To address these issues, we propose a novel visual-language causality-inspired framework named Cross-modal Causal Intervention with Mediator for Alzheimer's Disease Diagnosis (MediAD) for diagnostic assistance. Our MediAD employs Large Language Models (LLMs) to summarize clinical data under strict templates, therefore enriching textual inputs. The MediAD model utilizes Magnetic Resonance Imaging (MRI), clinical data, and textual data enriched by LLMs to classify participants into Cognitively Normal (CN), MCI, and AD categories. Because of the presence of confounders, such as cerebral vascular lesions and age-related biomarkers, non-causal models are likely to capture spurious input-output correlations, generating less reliable results. Our framework implicitly mitigates the effect of both observable and unobservable confounders through a unified causal intervention method. Experimental results demonstrate the outstanding performance of our method in distinguishing CN/MCI/AD cases, outperforming other methods in most evaluation metrics. The study showcases the potential of integrating causal reasoning with multi-modal learning for neurological disease diagnosis.

Haowen Xiao, Guanghui Liu, Xinyi Gao et al.

Self-supervised learning (SSL) has shown remarkable data representation capabilities across a wide range of datasets. However, when applied to real-world datasets with long-tailed distributions, performance on multiple downstream tasks degrades significantly. Recently, the community has begun to focus more on self-supervised long-tailed learning. Some works attempt to transfer temperature mechanisms to self-supervised learning or use category-space uniformity constraints to balance the representation of different categories in the embedding space to fight against long-tail distributions. However, most of these approaches focus on the joint optimization of all samples in the dataset or on constraining the category distribution, with little attention given to whether each individual sample is optimally guided during training. To address this issue, we propose Temperature Auxiliary Sample-level Encouragement (TASE). We introduce pseudo-labels into self-supervised long-tailed learning, utilizing pseudo-label information to drive a dynamic temperature and re-weighting strategy. Specifically, We assign an optimal temperature parameter to each sample. Additionally, we analyze the lack of quantity awareness in the temperature parameter and use re-weighting to compensate for this deficiency, thereby achieving optimal training patterns at the sample level. Comprehensive experimental results on six benchmarks across three datasets demonstrate that our method achieves outstanding performance in improving long-tail recognition, while also exhibiting high robustness.