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40 papers
Comparative Analysis of Deep Learning Strategies for Hypertensive Retinopathy Detection from Fundus Images: From Scratch and Pre-trained Models
Yanqiao Zhu
This paper presents a comparative analysis of deep learning strategies for detecting hypertensive retinopathy from fundus images, a central task in the HRDC challenge~\cite{qian202…
Bi-Level Graph Structure Learning for Next POI Recommendation
Liang Wang, Shu Wu, Qiang Liu +3
Next point-of-interest (POI) recommendation aims to predict a user's next destination based on sequential check-in history and a set of POI candidates. Graph neural networks (GNNs)…
MIRAI: Evaluating LLM Agents for Event Forecasting
Chenchen Ye, Ziniu Hu, Yihe Deng +4
Recent advancements in Large Language Models (LLMs) have empowered LLM agents to autonomously collect world information, over which to conduct reasoning to solve complex problems.…
Efficient Evolutionary Search Over Chemical Space with Large Language Models
Haorui Wang, Marta Skreta, Cher-Tian Ser +11
Molecular discovery, when formulated as an optimization problem, presents significant computational challenges because optimization objectives can be non-differentiable. Evolutiona…
BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers
Ran Xu, Wenqi Shi, Yue Yu +6
Developing effective biomedical retrieval models is important for excelling at knowledge-intensive biomedical tasks but still challenging due to the deficiency of sufficient public…
An Evaluation of Large Language Models in Bioinformatics Research
Hengchuang Yin, Zhonghui Gu, Fanhao Wang +6
Large language models (LLMs) such as ChatGPT have gained considerable interest across diverse research communities. Their notable ability for text completion and generation has ina…
GSLB: The Graph Structure Learning Benchmark
Zhixun Li, Liang Wang, Xin Sun +8
Graph Structure Learning (GSL) has recently garnered considerable attention due to its ability to optimize both the parameters of Graph Neural Networks (GNNs) and the computation g…
Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks
Yanqiao Zhu, Jeehyun Hwang, Keir Adams +10
Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are e…
Uncovering Neural Scaling Laws in Molecular Representation Learning
Dingshuo Chen, Yanqiao Zhu, Jieyu Zhang +5
Molecular Representation Learning (MRL) has emerged as a powerful tool for drug and materials discovery in a variety of tasks such as virtual screening and inverse design. While th…
SciBench: Evaluating College-Level Scientific Problem-Solving Abilities of Large Language Models
Xiaoxuan Wang, Ziniu Hu, Pan Lu +7
Most of the existing Large Language Model (LLM) benchmarks on scientific problem reasoning focus on problems grounded in high-school subjects and are confined to elementary algebra…
MHub: Unlocking the Potential of Machine Learning for Materials Discovery
Yuanqi Du, Yingheng Wang, Yining Huang +6
We introduce MHub, a toolkit for advancing machine learning in materials discovery. Machine learning has achieved remarkable progress in modeling molecular structures, especial…
Neighborhood-Regularized Self-Training for Learning with Few Labels
Ran Xu, Yue Yu, Hejie Cui +5
Training deep neural networks (DNNs) with limited supervision has been a popular research topic as it can significantly alleviate the annotation burden. Self-training has been succ…
A Survey on Pretrained Language Models for Neural Code Intelligence
Yichen Xu, Yanqiao Zhu
As the complexity of modern software continues to escalate, software engineering has become an increasingly daunting and error-prone endeavor. In recent years, the field of Neural…
Learning Task-Aware Effective Brain Connectivity for fMRI Analysis with Graph Neural Networks
Yue Yu, Xuan Kan, Hejie Cui +9
Functional magnetic resonance imaging (fMRI) has become one of the most common imaging modalities for brain function analysis. Recently, graph neural networks (GNN) have been adopt…
A Systematic Survey of Chemical Pre-trained Models
Jun Xia, Yanqiao Zhu, Yuanqi Du +1
Deep learning has achieved remarkable success in learning representations for molecules, which is crucial for various biochemical applications, ranging from property prediction to…
Code Recommendation for Open Source Software Developers
Yiqiao Jin, Yunsheng Bai, Yanqiao Zhu +2
Open Source Software (OSS) is forming the spines of technology infrastructures, attracting millions of talents to contribute. Notably, it is challenging and critical to consider bo…
Improving Molecular Pretraining with Complementary Featurizations
Yanqiao Zhu, Dingshuo Chen, Yuanqi Du +3
Molecular pretraining, which learns molecular representations over massive unlabeled data, has become a prominent paradigm to solve a variety of tasks in computational chemistry an…
Interpretable Graph Neural Networks for Connectome-Based Brain Disorder Analysis
Hejie Cui, Wei Dai, Yanqiao Zhu +3
Human brains lie at the core of complex neurobiological systems, where the neurons, circuits, and subsystems interact in enigmatic ways. Understanding the structural and functional…
Data-Efficient Brain Connectome Analysis via Multi-Task Meta-Learning
Yi Yang, Yanqiao Zhu, Hejie Cui +4
Brain networks characterize complex connectivities among brain regions as graph structures, which provide a powerful means to study brain connectomes. In recent years, graph neural…
BrainGB: A Benchmark for Brain Network Analysis with Graph Neural Networks
Hejie Cui, Wei Dai, Yanqiao Zhu +7
Mapping the connectome of the human brain using structural or functional connectivity has become one of the most pervasive paradigms for neuroimaging analysis. Recently, Graph Neur…
A Survey of Pretraining on Graphs: Taxonomy, Methods, and Applications
Jun Xia, Yanqiao Zhu, Yuanqi Du +1
Pretrained Language Models (PLMs) such as BERT have revolutionized the landscape of Natural Language Processing (NLP). Inspired by their proliferation, tremendous efforts have been…
A Survey on Deep Graph Generation: Methods and Applications
Yanqiao Zhu, Yuanqi Du, Yinkai Wang +4
Graphs are ubiquitous in encoding relational information of real-world objects in many domains. Graph generation, whose purpose is to generate new graphs from a distribution simila…
Latent Structure Mining with Contrastive Modality Fusion for Multimedia Recommendation
Jinghao Zhang, Yanqiao Zhu, Qiang Liu +3
Recent years have witnessed growing interests in multimedia recommendation, which aims to predict whether a user will interact with an item with multimodal contents. Previous studi…
An Empirical Study of Graph Contrastive Learning
Yanqiao Zhu, Yichen Xu, Qiang Liu +1
Graph Contrastive Learning (GCL) establishes a new paradigm for learning graph representations without human annotations. Although remarkable progress has been witnessed recently,…