A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding

Authors: Shen, Yiqing, Chen, Zan, Mamalakis, Michail, He, Luhan, Xia, Haiyang, Li, Tianbin, Su, Yanzhou, He, Junjun, Wang, Yu Guang

Source: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2024 IEEE International Conference on. :2390-2395 Dec, 2024

Relation: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

LaGDif: Latent Graph Diffusion Model for Efficient Protein Inverse Folding with Self-Ensemble

Authors: Wu, Taoyu, Wang, Yu Guang, Shen, Yiqing

Source: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2024 IEEE International Conference on. :3850-3855 Dec, 2024

Relation: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

A Regressor-Guided Graph Diffusion Model for Predicting Enzyme Mutations to Enhance Turnover Number

Authors: Yu, Xiaozhu, Yi, Kai, Wang, Yu Guang, Shen, Yiqing

Source: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2024 IEEE International Conference on. :3943-3948 Dec, 2024

Relation: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

TourSynbio: A Multi-Modal Large Model and Agent Framework to Bridge Text and Protein Sequences for Protein Engineering

Authors: Shen, Yiqing, Chen, Zan, Mamalakis, Michail, Liu, Yungeng, Li, Tianbin, Su, Yanzhou, He, Junjun, Lio, Pietro, Wang, Yu Guang

Source: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2024 IEEE International Conference on. :2382-2389 Dec, 2024

Relation: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

TourSynbio-Search: A Large Language Model Driven Agent Framework for Unified Search Method for Protein Engineering

Authors: Liu, Yungeng, Chen, Zan, Wang, Yu Guang, Shen, Yiqing

Source: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2024 IEEE International Conference on. :5395-5400 Dec, 2024

Relation: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Validation of an LLM-based Multi-Agent Framework for Protein Engineering in Dry Lab and Wet Lab

Authors: Chen, Zan, Liu, Yungeng, Wang, Yu Guang, Shen, Yiqing

Source: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2024 IEEE International Conference on. :5364-5370 Dec, 2024

Relation: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

FalconProtein: Finetuning Falcon Foundation Model for Protein Engineering

Authors: Yang, Wenjun, Shen, Yiqing, Wang, Zehong, Zhao, Rui, Lu, Qitong, Liu, Xinsheng, Liu, Yungeng, Debbah, Merouane, Wang, Yu Guang, Li Wang, Shir

Source: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2024 IEEE International Conference on. :5409-5417 Dec, 2024

Relation: 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Score-matching-based Structure Learning for Temporal Data on Networks

Authors: Chen, Hao, Yi, Kai, Liu, Lin, Wang, Yu Guang

Subject Terms: Statistics - Machine Learning, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2412.07469

AutoProteinEngine: A Large Language Model Driven Agent Framework for Multimodal AutoML in Protein Engineering

Authors: Liu, Yungeng, Chen, Zan, Wang, Yu Guang, Shen, Yiqing

Subject Terms: Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2411.04440

A Survey for Large Language Models in Biomedicine

Authors: Wang, Chong, Li, Mengyao, He, Junjun, Wang, Zhongruo, Darzi, Erfan, Chen, Zan, Ye, Jin, Li, Tianbin, Su, Yanzhou, Ke, Jing, Qu, Kaili, Li, Shuxin, Yu, Yi, Liò, Pietro, Wang, Tianyun, Wang, Yu Guang, Shen, Yiqing

Subject Terms: Computer Science - Computation and Language, Computer Science - Artificial Intelligence

Access URL: http://arxiv.org/abs/2409.00133

How GNNs Facilitate CNNs in Mining Geometric Information from Large-Scale Medical Images

Authors: Shen, Yiqing, Zhou, Bingxin, Xiong, Xinye, Gao, Ruitian, Wang, Yu Guang

Source: 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) Bioinformatics and Biomedicine (BIBM), 2023 IEEE International Conference on. :2227-2230 Dec, 2023

Relation: 2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Limiting Over-Smoothing and Over-Squashing of Graph Message Passing by Deep Scattering Transforms

Authors: Jiang, Yuanhong, Zou, Dongmian, Zhang, Xiaoqun, Wang, Yu Guang

Subject Terms: Mathematics - Spectral Theory

Access URL: http://arxiv.org/abs/2407.06988

Improving Antibody Design with Force-Guided Sampling in Diffusion Models

Authors: Kulytė, Paulina, Vargas, Francisco, Mathis, Simon Valentin, Wang, Yu Guang, Hernández-Lobato, José Miguel, Liò, Pietro

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Machine Learning, Quantitative Biology - Biomolecules

Access URL: http://arxiv.org/abs/2406.05832

How Universal Polynomial Bases Enhance Spectral Graph Neural Networks: Heterophily, Over-smoothing, and Over-squashing

Authors: Huang, Keke, Wang, Yu Guang, Li, Ming, Liò, and Pietro

Subject Terms: Computer Science - Machine Learning, Computer Science - Social and Information Networks

Access URL: http://arxiv.org/abs/2405.12474

EqMotion: Equivariant Multi-Agent Motion Prediction with Invariant Interaction Reasoning

Authors: Xu, Chenxin, Tan, Robby T., Tan, Yuhong, Chen, Siheng, Wang, Yu Guang, Wang, Xinchao, Wang, Yanfeng

Source: 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) CVPR Computer Vision and Pattern Recognition (CVPR), 2023 IEEE/CVF Conference on. :1410-1420 Jun, 2023

Relation: 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)

Adaptive Importance Sampling and Quasi-Monte Carlo Methods for 6G URLLC Systems

Authors: Ke, Xiongwen, Zhu, Houying, Yi, Kai, He, Gaoning, Yang, Ganghua, Wang, Yu Guang

Source: ICC 2023 - IEEE International Conference on Communications Communications, ICC 2023 - IEEE International Conference on. :5272-5278 May, 2023

Relation: ICC 2023 - IEEE International Conference on Communications

ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering

Authors: Shen, Yiqing, Lv, Outongyi, Zhu, Houying, Wang, Yu Guang

Subject Terms: Quantitative Biology - Biomolecules, Computer Science - Artificial Intelligence, Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2405.06658

Layer-diverse Negative Sampling for Graph Neural Networks

Authors: Duan, Wei, Lu, Jie, Wang, Yu Guang, Xuan, Junyu

Subject Terms: Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2403.11408

Dirichlet Energy Enhancement of Graph Neural Networks by Framelet Augmentation

Authors: Chen, Jialin, Wang, Yuelin, Bodnar, Cristian, Ying, Rex, Lio, Pietro, Wang, Yu Guang

Subject Terms: Computer Science - Machine Learning

Access URL: http://arxiv.org/abs/2311.05767

Oversquashing in GNNs through the lens of information contraction and graph expansion

Authors: Banerjee, Pradeep Kr., Karhadkar, Kedar, Wang, Yu Guang, Alon, Uri, Montufar, Guido

Source: 2022 58th Annual Allerton Conference on Communication, Control, and Computing (Allerton) Communication, Control, and Computing (Allerton), 2022 58th Annual Allerton Conference on. :1-8 Sep, 2022

Relation: 2022 58th Annual Allerton Conference on Communication, Control, and Computing (Allerton)