27 citations · 29 across the 14 of their papers we have counts for
14 papers
Learning Molecular Representations from Cellular Phenotypes with Structure Preservation
Xuan Lin, Jingyu Sheng, Tengfei Ma +2
Phenotypic drug discovery enables the discovery of functional relationships between molecular structures and cellular responses. However, existing multimodal representation learnin…
Agents on a Tree: Pathwise Coordination for Multi-Objective Molecular Optimization
Jia Zhang, Tengfei Ma, Tianle Li +3
Multi-objective molecular optimization requires searching vast chemical spaces under conflicting objectives, where early design decisions strongly constrain downstream outcomes. Ex…
CryoProt: A Protein Pretraining Framework with Cross-Box Interactions on Cryo-EM Density Maps
Dan Luo, Xuan Lin, Peng Zhou +4
Despite the growing availability of cryo-electron microscopy (cryo-EM) density maps, effectively leveraging them for protein representation remains challenging. First, current meth…
SpecX: A Large-Scale Benchmark for Multi-Modal Spectroscopy and Cross-Paradigm Evaluation
Chengrui Xiang, Tengfei Ma, Yujie Chen +3
Existing spectral benchmarks are limited in scale, modality alignment, and evaluation scope, and typically focus on either specialized models or multimodal language models (MLLMs).…
Sparse Task Vector Mixup with Hypernetworks for Efficient Knowledge Transfer in Whole-Slide Image Prognosis
Pei Liu, Xiangxiang Zeng, Tengfei Ma +3
Whole-Slide Images (WSIs) are widely used for estimating the prognosis of cancer patients. Current studies generally follow a cancer-specific learning paradigm. However, the availa…
DeepDR: an integrated deep-learning model web server for drug repositioning
Shuting Jin, Yi Jiang, Yimin Liu +5
Background: Identifying new indications for approved drugs is a complex and time-consuming process that requires extensive knowledge of pharmacology, clinical data, and advanced co…
MolBridge: Atom-Level Joint Graph Refinement for Robust Drug-Drug Interaction Event Prediction
Xuan Lin, Aocheng Ding, Tengfei Ma +2
Drug combinations offer therapeutic benefits but also carry the risk of adverse drug-drug interactions (DDIs), especially under complex molecular structures. Accurate DDI event pre…
From Knowledge to Treatment: Large Language Model Assisted Biomedical Concept Representation for Drug Repurposing
Chengrui Xiang, Tengfei Ma, Xiangzheng Fu +3
Drug repurposing plays a critical role in accelerating treatment discovery, especially for complex and rare diseases. Biomedical knowledge graphs (KGs), which encode rich clinical…
ImageDDI: Image-enhanced Molecular Motif Sequence Representation for Drug-Drug Interaction Prediction
Yuqin He, Tengfei Ma, Chaoyi Li +6
To mitigate the potential adverse health effects of simultaneous multi-drug use, including unexpected side effects and interactions, accurately identifying and predicting drug-drug…
AdaptMol: Adaptive Fusion from Sequence String to Topological Structure for Few-shot Drug Discovery
Yifan Dai, Xuanbai Ren, Tengfei Ma +4
Accurate molecular property prediction (MPP) is a critical step in modern drug development. However, the scarcity of experimental validation data poses a significant challenge to A…
SDN: Learning to Denoise Unconvincing Knowledge for Inductive Knowledge Graph Completion
Tengfei Ma, Yujie Chen, Liang Wang +3
Inductive Knowledge Graph Completion (KGC) aims to infer missing facts between newly emerged entities within knowledge graphs (KGs), posing a significant challenge. While recent st…
Y-Mol: A Multiscale Biomedical Knowledge-Guided Large Language Model for Drug Development
Tengfei Ma, Xuan Lin, Tianle Li +8
Large Language Models (LLMs) have recently demonstrated remarkable performance in general tasks across various fields. However, their effectiveness within specific domains such as…
KGExplainer: Towards Exploring Connected Subgraph Explanations for Knowledge Graph Completion
Tengfei Ma, Xiang song, Wen Tao +6
Knowledge graph completion (KGC) aims to alleviate the inherent incompleteness of knowledge graphs (KGs), which is a critical task for various applications, such as recommendations…
Learning to Denoise Biomedical Knowledge Graph for Robust Molecular Interaction Prediction
Tengfei Ma, Yujie Chen, Wen Tao +9
Molecular interaction prediction plays a crucial role in forecasting unknown interactions between molecules, such as drug-target interaction (DTI) and drug-drug interaction (DDI),…