Search Results for author: Yingzhou Lu

Found 14 papers, 6 papers with code

Gradient GA: Gradient Genetic Algorithm for Drug Molecular Design

1 code implementation14 Feb 2025 Chris Zhuang, Debadyuti Mukherjee, Yingzhou Lu, Tianfan Fu, Ruqi Zhang

To address this limitation, we propose a novel approach called Gradient Genetic Algorithm (Gradient GA), which incorporates gradient information from the objective function into genetic algorithms.

Protein-Mamba: Biological Mamba Models for Protein Function Prediction

no code implementations22 Sep 2024 Bohao Xu, Yingzhou Lu, Yoshitaka Inoue, Namkyeong Lee, Tianfan Fu, Jintai Chen

Protein function prediction is a pivotal task in drug discovery, significantly impacting the development of effective and safe therapeutics.

Drug Discovery Mamba +3

SMILES-Mamba: Chemical Mamba Foundation Models for Drug ADMET Prediction

no code implementations11 Aug 2024 Bohao Xu, Yingzhou Lu, Chenhao Li, Ling Yue, Xiao Wang, Nan Hao, Tianfan Fu, Jim Chen

In drug discovery, predicting the absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of small-molecule drugs is critical for ensuring safety and efficacy.

Drug Discovery Mamba +3

BioMamba: A Pre-trained Biomedical Language Representation Model Leveraging Mamba

1 code implementation5 Aug 2024 Ling Yue, Sixue Xing, Yingzhou Lu, Tianfan Fu

BioMamba builds upon the Mamba architecture and is pre-trained on an extensive corpus of biomedical literature.

Mamba

DrugCLIP: Contrastive Drug-Disease Interaction For Drug Repurposing

no code implementations2 Jul 2024 Yingzhou Lu, Yaojun Hu, Chenhao Li

Bringing a novel drug from the original idea to market typically requires more than ten years and billions of dollars.

Contrastive Learning

TrialBench: Multi-Modal Artificial Intelligence-Ready Clinical Trial Datasets

1 code implementation30 Jun 2024 Jintai Chen, Yaojun Hu, Yue Wang, Yingzhou Lu, Xu Cao, Miao Lin, Hongxia Xu, Jian Wu, Cao Xiao, Jimeng Sun, Lucas Glass, Kexin Huang, Marinka Zitnik, Tianfan Fu

Clinical trials are pivotal for developing new medical treatments, yet they typically pose some risks such as patient mortality, adverse events, and enrollment failure that waste immense efforts spanning over a decade.

Structure-based Drug Design Benchmark: Do 3D Methods Really Dominate?

1 code implementation4 Jun 2024 Kangyu Zheng, Yingzhou Lu, Zaixi Zhang, Zhongwei Wan, Yao Ma, Marinka Zitnik, Tianfan Fu

Currently, the field of structure-based drug design is dominated by three main types of algorithms: search-based algorithms, deep generative models, and reinforcement learning.

Drug Design

Uncertainty Quantification on Clinical Trial Outcome Prediction

1 code implementation7 Jan 2024 Tianyi Chen, Yingzhou Lu, Nan Hao, Yuanyuan Zhang, Capucine van Rechem, Jintai Chen, Tianfan Fu

Selective classification, encompassing a spectrum of methods for uncertainty quantification, empowers the model to withhold decision-making in the face of samples marked by ambiguity or low confidence, thereby amplifying the accuracy of predictions for the instances it chooses to classify.

Decision Making Drug Discovery +3

GenoCraft: A Comprehensive, User-Friendly Web-Based Platform for High-Throughput Omics Data Analysis and Visualization

1 code implementation21 Dec 2023 Yingzhou Lu, Minjie Shen, Ling Yue, Chenhao Li, Lulu Chen, Fan Meng, Xiao Wang, David Herrington, Yue Wang, Yue Zhao, Tianfan Fu, Capucine van Rechem

With GenoCraft, researchers and data scientists have access to an array of cutting-edge bioinformatics tools under a user-friendly interface, making it a valuable resource for managing and analyzing large-scale omics data.

Machine Learning for Synthetic Data Generation: A Review

no code implementations8 Feb 2023 Yingzhou Lu, Minjie Shen, Huazheng Wang, Xiao Wang, Capucine van Rechem, Tianfan Fu, Wenqi Wei

In light of these challenges, the concept of synthetic data generation emerges as a promising alternative that allows for data sharing and utilization in ways that real-world data cannot facilitate.

Fairness Synthetic Data Generation

Deep Learning based Multi-Label Image Classification of Protest Activities

no code implementations10 Jan 2023 Yingzhou Lu, Kosaku Sato, Jialu Wang

With the rise of internet technology amidst increasing rates of urbanization, sharing information has never been easier thanks to globally-adopted platforms for digital communication.

Deep Learning Multi-Label Image Classification

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