32 citations · 97 across the 27 of their papers we have counts for
14 papers · 1 filter
Artificial Intelligence for Central Dogma-Centric Multi-Omics: Challenges and Breakthroughs
Lei Xin, Caiyun Huang, Hao Li +8
With the rapid development of high-throughput sequencing platforms, an increasing number of omics technologies, such as genomics, metabolomics, and transcriptomics, are being appli…
Unveiling the Backbone-Optimizer Coupling Bias in Visual Representation Learning
Siyuan Li, Juanxi Tian, Zedong Wang +6
This paper delves into the interplay between vision backbones and optimizers, unvealing an inter-dependent phenomenon termed \textit{\textbf{b}ackbone-\textbf{o}ptimizer \textbf{c}…
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…
GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models
Zicheng Liu, Jiahui Li, Siyuan Li +5
The Genomic Foundation Model (GFM) paradigm is expected to facilitate the extraction of generalizable representations from massive genomic data, thereby enabling their application…
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…
PPFlow: Target-aware Peptide Design with Torsional Flow Matching
Haitao Lin, Odin Zhang, Huifeng Zhao +5
Therapeutic peptides have proven to have great pharmaceutical value and potential in recent decades. However, methods of AI-assisted peptide drug discovery are not fully explored.…
LongVQ: Long Sequence Modeling with Vector Quantization on Structured Memory
Zicheng Liu, Li Wang, Siyuan Li +3
Transformer models have been successful in various sequence processing tasks, but the self-attention mechanism's computational cost limits its practicality for long sequences. Alth…
Advances of Deep Learning in Protein Science: A Comprehensive Survey
Bozhen Hu, Cheng Tan, Lirong Wu +7
Protein representation learning plays a crucial role in understanding the structure and function of proteins, which are essential biomolecules involved in various biological proces…
PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction
Lirong Wu, Yufei Huang, Cheng Tan +5
Compound-Protein Interaction (CPI) prediction aims to predict the pattern and strength of compound-protein interactions for rational drug discovery. Existing deep learning-based me…
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…