48 citations · 288 across the 47 of their papers we have counts for
48 papers
VecFormer: Towards Efficient and Generalizable Graph Transformer with Graph Token Attention
Jingbo Zhou, Jun Xia, Siyuan Li +11
Graph Transformer has demonstrated impressive capabilities in the field of graph representation learning. However, existing approaches face two critical challenges: (1) most models…
Multimodal Regression for Enzyme Turnover Rates Prediction
Bozhen Hu, Cheng Tan, Siyuan Li +4
The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most org…
ResearchPulse: Building Method-Experiment Chains through Multi-Document Scientific Inference
Qi Chen, Jingxuan Wei, Zhuoya Yao +5
Understanding how scientific ideas evolve requires more than summarizing individual papers-it demands structured, cross-document reasoning over thematically related research. In th…
SketchAgent: Generating Structured Diagrams from Hand-Drawn Sketches
Cheng Tan, Qi Chen, Jingxuan Wei +6
Hand-drawn sketches are a natural and efficient medium for capturing and conveying ideas. Despite significant advancements in controllable natural image generation, translating fre…
AlphaFold Database Debiasing for Robust Inverse Folding
Cheng Tan, Zhenxiao Cao, Zhangyang Gao +3
The AlphaFold Protein Structure Database (AFDB) offers unparalleled structural coverage at near-experimental accuracy, positioning it as a valuable resource for data-driven protein…
From Words to Structured Visuals: A Benchmark and Framework for Text-to-Diagram Generation and Editing
Jingxuan Wei, Cheng Tan, Qi Chen +6
We introduce the task of text-to-diagram generation, which focuses on creating structured visual representations directly from textual descriptions. Existing approaches in text-to-…
MeToken: Uniform Micro-environment Token Boosts Post-Translational Modification Prediction
Cheng Tan, Zhenxiao Cao, Zhangyang Gao +6
Post-translational modifications (PTMs) profoundly expand the complexity and functionality of the proteome, regulating protein attributes and interactions that are crucial for biol…
A Survey on Mixup Augmentations and Beyond
Xin Jin, Hongyu Zhu, Siyuan Li +6
As Deep Neural Networks have achieved thrilling breakthroughs in the past decade, data augmentations have garnered increasing attention as regularization techniques when massive la…
Short-Long Convolutions Help Hardware-Efficient Linear Attention to Focus on Long Sequences
Zicheng Liu, Siyuan Li, Li Wang +3
To mitigate the computational complexity in the self-attention mechanism on long sequences, linear attention utilizes computation tricks to achieve linear complexity, while state s…
Peer Review as A Multi-Turn and Long-Context Dialogue with Role-Based Interactions
Cheng Tan, Dongxin Lyu, Siyuan Li +5
Large Language Models (LLMs) have demonstrated wide-ranging applications across various fields and have shown significant potential in the academic peer-review process. However, ex…
VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling
Siyuan Li, Zedong Wang, Zicheng Liu +5
Similar to natural language models, pre-trained genome language models are proposed to capture the underlying intricacies within genomes with unsupervised sequence modeling. They h…
CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph
Haitao Lin, Guojiang Zhao, Odin Zhang +7
Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. How…
Retrieval Meets Reasoning: Even High-school Textbook Knowledge Benefits Multimodal Reasoning
Cheng Tan, Jingxuan Wei, Linzhuang Sun +5
Large language models equipped with retrieval-augmented generation (RAG) represent a burgeoning field aimed at enhancing answering capabilities by leveraging external knowledge bas…
UniIF: Unified Molecule Inverse Folding
Zhangyang Gao, Jue Wang, Cheng Tan +5
Molecule inverse folding has been a long-standing challenge in chemistry and biology, with the potential to revolutionize drug discovery and material science. Despite specified mod…
Learning to Predict Mutation Effects of Protein-Protein Interactions by Microenvironment-aware Hierarchical Prompt Learning
Lirong Wu, Yijun Tian, Haitao Lin +4
Protein-protein bindings play a key role in a variety of fundamental biological processes, and thus predicting the effects of amino acid mutations on protein-protein binding is cru…
MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding
Lirong Wu, Yijun Tian, Yufei Huang +4
Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays r…
Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge
Yufei Huang, Odin Zhang, Lirong Wu +5
Accurate prediction of protein-ligand binding structures, a task known as molecular docking is crucial for drug design but remains challenging. While deep learning has shown promis…
Switch EMA: A Free Lunch for Better Flatness and Sharpness
Siyuan Li, Zicheng Liu, Juanxi Tian +9
Exponential Moving Average (EMA) is a widely used weight averaging (WA) regularization to learn flat optima for better generalizations without extra cost in deep neural network (DN…
Masked Modeling for Self-supervised Representation Learning on Vision and Beyond
Siyuan Li, Luyuan Zhang, Zedong Wang +8
As the deep learning revolution marches on, self-supervised learning has garnered increasing attention in recent years thanks to its remarkable representation learning ability and…
Progressive Multi-Modality Learning for Inverse Protein Folding
Jiangbin Zheng, Stan Z. Li
While deep generative models show promise for learning inverse protein folding directly from data, the lack of publicly available structure-sequence pairings limits their generaliz…
Boosting the Power of Small Multimodal Reasoning Models to Match Larger Models with Self-Consistency Training
Cheng Tan, Jingxuan Wei, Zhangyang Gao +5
Multimodal reasoning is a challenging task that requires models to reason across multiple modalities to answer questions. Existing approaches have made progress by incorporating la…
Protein 3D Graph Structure Learning for Robust Structure-based Protein Property Prediction
Yufei Huang, Siyuan Li, Jin Su +9
Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimati…
USTEP: Spatio-Temporal Predictive Learning under A Unified View
Cheng Tan, Jue Wang, Zhangyang Gao +2
Spatio-temporal predictive learning plays a crucial role in self-supervised learning, with wide-ranging applications across a diverse range of fields. Previous approaches for tempo…
SemiReward: A General Reward Model for Semi-supervised Learning
Siyuan Li, Weiyang Jin, Zedong Wang +4
Semi-supervised learning (SSL) has witnessed great progress with various improvements in the self-training framework with pseudo labeling. The main challenge is how to distinguish…