Publications (50)
Non-zero Integral Spin of Acoustic Vortices and Spin-orbit Interaction in Longitudinal Acoustics
Wei Wang, Yang Tan, Jingjing Liu +2
Spin and orbital angular momenta (AM) are of fundamental interest in wave physics. Acoustic wave, as a typical longitudinal wave, has been well studied in terms of orbital AM, but…
Exploiting Task Relationships in Continual Learning via Transferability-Aware Task Embeddings
Yanru Wu, Jianning Wang, Xiangyu Chen +4
Continual learning (CL) has been a critical topic in contemporary deep neural network applications, where higher levels of both forward and backward transfer are desirable for an e…
Probabilistic Temporal Masked Attention for Cross-view Online Action Detection
Liping Xie, Yang Tan, Shicheng Jing +2
As a critical task in video sequence classification within computer vision, Online Action Detection (OAD) has garnered significant attention. The sensitivity of mainstream OAD mode…
Coherence Properties of Rare-Earth Spins in Micrometer-Thin Films
Zihua Chai, Zhaocong Wang, Xinghang Chen +8
Rare-earth ions in bulk crystals are excellent solid-state quantum systems in quantum information science, owing to the exceptional optical and spin coherence properties. However,…
Toward Temporal Realism in City-Scale Crisis Response Simulation using LLM Agents
Anping Zhang, Yang Tan, Yuanbo Tang +4
Human collective participation is rarely steady in time: it is bursty, with short episodes of intense activity separated by long quiet intervals. In crisis response and community m…
Fast and Interpretable Protein Substructure Alignment via Optimal Transport
Zhiyu Wang, Bingxin Zhou, Jing Wang +4
Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure…
VenusFactory: A Unified Platform for Protein Engineering Data Retrieval and Language Model Fine-Tuning
Yang Tan, Chen Liu, Jingyuan Gao +8
Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (P…
Tuning of Interlayer Coupling in Large-Area Graphene/WSe2 van der Waals Heterostructure via Ion Irradiation: Optical Evidences and Photonic Applications
Yang Tan, Xiaobiao Liu, Zhiliang He +4
Van der Waals (vdW) heterostructures are receiving great attentions due to their intriguing properties and potentials in many research fields. The flow of charge carriers in vdW he…
Sequence-Only Prediction of Binding Affinity Changes: A Robust and Interpretable Model for Antibody Engineering
Chen Liu, Mingchen Li, Yang Tan +3
A pivotal area of research in antibody engineering is to find effective modifications that enhance antibody-antigen binding affinity. Traditional wet-lab experiments assess mutants…
OTCE: A Transferability Metric for Cross-Domain Cross-Task Representations
Yang Tan, Yang Li, Shao-Lun Huang
Transfer learning across heterogeneous data distributions (a.k.a. domains) and distinct tasks is a more general and challenging problem than conventional transfer learning, where e…
Giant Acoustic Geometric Spin and Orbital Hall Effect
Wei Wang, Yang Tan, Jingjing Liu +2
Acoustic waves in fluid with spin-0 nature have been long believed not to support spin Hall effect and strong orbital Hall effect that enables experimental observation. Here we rep…
Layer compression and enhanced optical properties of few-layer graphene nanosheets induced by ion irradiation
Yang Tan, Zhen Shang, Shavkat Akhmadaliev +2
Graphene has been recognized as an attractive two-dimensional material for fundamental research and wide applications in electronic and photonic devices owing to its unique propert…
MALT: Multi-scale Action Learning Transformer for Online Action Detection
Zhipeng Yang, Ruoyu Wang, Yang Tan +1
Online action detection (OAD) aims to identify ongoing actions from streaming video in real-time, without access to future frames. Since these actions manifest at varying scales of…
Transferability-Guided Cross-Domain Cross-Task Transfer Learning
Yang Tan, Enming Zhang, Yang Li +2
We propose two novel transferability metrics F-OTCE (Fast Optimal Transport based Conditional Entropy) and JC-OTCE (Joint Correspondence OTCE) to evaluate how much the source model…
Practical Transferability Estimation for Image Classification Tasks
Yang Tan, Yang Li, Shao-Lun Huang
Transferability estimation is an essential problem in transfer learning to predict how good the performance is when transferring a source model (or source task) to a target task. R…
ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks
Dongxin Ye, Fang Hu, Han Hu +6
Nucleotide sequences constitute the fundamental genetic basis of biological systems, rendering viral genomic analysis critical for biomedical advancement. Despite progress in biolo…
Shapley-Guided Neural Repair Approach via Derivative-Free Optimization
Xinyu Sun, Wanwei Liu, Haoang Chi +7
DNNs are susceptible to defects like backdoors, adversarial attacks, and unfairness, undermining their reliability. Existing approaches mainly involve retraining, optimization, con…
TMT: Cross-domain Semantic Segmentation with Region-adaptive Transferability Estimation
Enming Zhang, Zhengyu Li, Yanru Wu +5
Recent advances in Vision Transformers (ViTs) have significantly advanced semantic segmentation performance. However, their adaptation to new target domains remains challenged by d…
Pro-PRIME: A general Temperature-Guided Language model to engineer enhanced Stability and Activity in Proteins
Fan Jiang, Mingchen Li, Jiajun Dong +23
Designing protein mutants of both high stability and activity is a critical yet challenging task in protein engineering. Here, we introduce PRIME, a deep learning model, which can…
Justlookup: One Millisecond Deep Feature Extraction for Point Clouds By Lookup Tables
Hongxin Lin, Zelin Xiao, Yang Tan +2
Deep models are capable of fitting complex high dimensional functions while usually yielding large computation load. There is no way to speed up the inference process by classical…
Understanding Knowledge Transferability for Transfer Learning: A Survey
Haohua Wang, Jingge Wang, Zijie Zhao +9
Transfer learning has become an essential paradigm in artificial intelligence, enabling the transfer of knowledge from a source task to improve performance on a target task. This a…
A PLMs based protein retrieval framework
Yuxuan Wu, Xiao Yi, Yang Tan +3
Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search…
A Comprehensive Survey on Heart Sound Analysis in the Deep Learning Era
Zhao Ren, Yi Chang, Thanh Tam Nguyen +3
Heart sound auscultation has been applied in clinical usage for early screening of cardiovascular diseases. Due to the high demand for auscultation expertise, automatic auscultatio…
Four-Dimensional Higher-Order Chern Insulator and Its Acoustic Realization
Ze-Guo Chen, Weiwei Zhu, Yang Tan +2
We present a theoretical study and experimental realization of a system that is simultaneously a four-dimensional (4D) Chern insulator and a higher-order topological insulator (HOT…
AdaSR: Adaptive Streaming Reasoning with Hierarchical Relative Policy Optimization
Junlong Tong, Wenqi Xu, Yingqi Fan +4
Large reasoning models typically follow a read-then-think paradigm: they observe the complete input, reason over a static context, and then produce the answer. Yet many real-world…
Multi-level Protein Representation Learning for Blind Mutational Effect Prediction
Yang Tan, Bingxin Zhou, Yuanhong Jiang +2
Directed evolution plays an indispensable role in protein engineering that revises existing protein sequences to attain new or enhanced functions. Accurately predicting the effects…
VenusMutHub: A systematic evaluation of protein mutation effect predictors on small-scale experimental data
Liang Zhang, Hua Pang, Chenghao Zhang +11
In protein engineering, while computational models are increasingly used to predict mutation effects, their evaluations primarily rely on high-throughput deep mutational scanning (…
Rank-and-Reason: Multi-Agent Collaboration Accelerates Zero-Shot Protein Mutation Prediction
Yang Tan, Yuanxi Yu, Can Wu +7
Zero-shot mutation prediction is vital for low-resource protein engineering, yet existing protein language models (PLMs) often yield statistically confident results that ignore fun…
Retrieval-Enhanced Mutation Mastery: Augmenting Zero-Shot Prediction of Protein Language Model
Yang Tan, Ruilin Wang, Banghao Wu +2
Enzyme engineering enables the modification of wild-type proteins to meet industrial and research demands by enhancing catalytic activity, stability, binding affinities, and other…
Hopping Transfer Optimizes Avalanche Multiplication in Molybdenum Disulfide
Xiaofan Cai, Ruichang Chen, Xu Gao +6
Recently, avalanche multiplication has been observed in TMDC-based FETs, enhancing sensor performance with high sensitivity. However, the high voltage required for operation can da…
Face Recognition from Sequential Sparse 3D Data via Deep Registration
Yang Tan, Hongxin Lin, Zelin Xiao +2
Previous works have shown that face recognition with high accurate 3D data is more reliable and insensitive to pose and illumination variations. Recently, low-cost and portable 3D…
Self-evolving AI agents for protein discovery and directed evolution
Yang Tan, Lingrong Zhang, Mingchen Li +5
Protein scientific discovery is bottlenecked by the manual orchestration of information and algorithms, while general agents are insufficient in complex domain projects. VenusFacto…
PETA: Evaluating the Impact of Protein Transfer Learning with Sub-word Tokenization on Downstream Applications
Yang Tan, Mingchen Li, Pan Tan +4
Large protein language models are adept at capturing the underlying evolutionary information in primary structures, offering significant practical value for protein engineering. Co…
Single-sensor and real-time ultrasonic imaging using an AI-driven disordered metasurface
Wei Wang, Jie Hu, Jingjing Liu +5
Non-destructive testing and medical diagnostic techniques using ultrasound has become indispensable in evaluating the state of materials or imaging the internal human body, respect…
ViCoStream: Streaming VideoLLMs Can Run Beyond 100 FPS with Stage-Wise Coordinated Inference
Yang Tan, Junlong Tong, Linan Yue +3
Streaming VideoLLMs must continuously process incoming video while maintaining low query latency, making both video-ingestion throughput and query-time responsiveness critical for…
Secondary Structure-Guided Novel Protein Sequence Generation with Latent Graph Diffusion
Yutong Hu, Yang Tan, Andi Han +3
The advent of deep learning has introduced efficient approaches for de novo protein sequence design, significantly improving success rates and reducing development costs compared t…
Mistakes of A Popular Protocol Calculating Private Set Intersection and Union Cardinality and Its Corrections
Yang Tan, Bo Lv
In 2012, De Cristofaro et al. proposed a protocol to calculate the Private Set Intersection and Union cardinality(PSI-CA and PSU-CA). This protocol's security is based on the famou…
CPE-Pro: A Structure-Sensitive Deep Learning Method for Protein Representation and Origin Evaluation
Wenrui Gou, Wenhui Ge, Yang Tan +3
Protein structures are important for understanding their functions and interactions. Currently, many protein structure prediction methods are enriching the structure database. Disc…
Immunogenicity Prediction with Dual Attention Enables Vaccine Target Selection
Song Li, Yang Tan, Song Ke +2
Immunogenicity prediction is a central topic in reverse vaccinology for finding candidate vaccines that can trigger protective immune responses. Existing approaches typically rely…
Transfer Risk Map: Mitigating Pixel-level Negative Transfer in Medical Segmentation
Shutong Duan, Jingyun Yang, Yang Tan +3
How to mitigate negative transfer in transfer learning is a long-standing and challenging issue, especially in the application of medical image segmentation. Existing methods for r…
Finding the Most Transferable Tasks for Brain Image Segmentation
Yicong Li, Yang Tan, Jingyun Yang +2
Although many studies have successfully applied transfer learning to medical image segmentation, very few of them have investigated the selection strategy when multiple source task…
Ultrasensitive biosensor based on Nd:YAG waveguide laser: Tumor cell and Dextrose solution
Guanhua Li, Huiyuan Li, Rumei Gong +3
This work demonstrates the Nd:YAG waveguide laser as an efficient platform for the bio-sensing. The waveguide was fabricated in the Nd:YAG crystal by the cooperation of the ultrafa…
VenusX: Unlocking Fine-Grained Functional Understanding of Proteins
Yang Tan, Wenrui Gou, Bozitao Zhong +3
Deep learning models have driven significant progress in predicting protein function and interactions at the protein level. While these advancements have been invaluable for many b…
Simple, Efficient and Scalable Structure-aware Adapter Boosts Protein Language Models
Yang Tan, Mingchen Li, Bingxin Zhou +7
Fine-tuning Pre-trained protein language models (PLMs) has emerged as a prominent strategy for enhancing downstream prediction tasks, often outperforming traditional supervised lea…
MedChatZH: a Better Medical Adviser Learns from Better Instructions
Yang Tan, Mingchen Li, Zijie Huang +2
Generative large language models (LLMs) have shown great success in various applications, including question-answering (QA) and dialogue systems. However, in specialized domains li…
Transferability Estimation for Semantic Segmentation Task
Yang Tan, Yang Li, Shao-Lun Huang
Transferability estimation is a fundamental problem in transfer learning to predict how good the performance is when transferring a source model (or source task) to a target task.…
Team PA-VCG's Solution for Competition on Understanding Chinese College Entrance Exam Papers in ICDAR'25
Wei Wu, Wenjie Wang, Yang Tan +6
This report presents Team PA-VGG's solution for the ICDAR'25 Competition on Understanding Chinese College Entrance Exam Papers. In addition to leveraging high-resolution image proc…
Smart Cameras
David J. Brady, Minghao Hu, Chengyu Wang +6
We review camera architecture in the age of artificial intelligence. Modern cameras use physical components and software to capture, compress and display image data. Over the past…
ProtSolM: Protein Solubility Prediction with Multi-modal Features
Yang Tan, Jia Zheng, Liang Hong +1
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs…
Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance?
Yang Tan, Lirong Zheng, Bozitao Zhong +2
Deep learning has become a crucial tool in studying proteins. While the significance of modeling protein structure has been discussed extensively in the literature, amino acid type…