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Hongbin Ye

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4 papers

2 author rows

AAAI Conference 2026 Conference Paper

Synergizing Multigrid Algorithms with Vision Transformer: A Novel Approach to Enhance the Seismic Foundation Model

Huiwen Wu
Shuo Zhang
Yi Liu
Hongbin Ye

Due to the rapid advancement and homogenization of Artificial Intelligence (AI) technology development, transformer-based foundation models have revolutionized scientific applications, such as drug discovery, materials research, and astronomy. However, seismic data presents unique characteristics that require specialized processing techniques for pretraining foundation models in seismic contexts with high- and low-frequency features playing crucial roles. Existing Vision Transformer (ViT) with sequential image tokenization fails to efficiently and effectively capture both high- and low-frequency seismic information because they ignore the intrinsic structural patterns of seismograms. This work introduces ADATG, a novel adaptive two-grid training strategy with Hilbert encoding, explicitly tailored for seismogram data and leveraging the hierarchical structures inherent in seismic data. Specifically, our approach employs spectrum decomposition to separate high- and low-frequency components, and hierarchical Hilbert encoding to represent the data effectively. Moreover, inspired by the frequency principle, we propose an adaptive training strategy that initially emphasizes coarse-level information and then progressively refines the model's focus on fine-level features. Extensive experiments demonstrate the effectiveness and efficiency of our method. This research highlights the importance of data encoding and training strategies informed by the distinct characteristics of high- and low-frequency features in seismic images, ultimately enhancing the pretraining of visual seismic foundation models.

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ECAI Conference 2023 Conference Paper

Active Finetuning Protein Language Model: A Budget-Friendly Method for Directed Evolution

Ming Qin
Keyan Ding
Bin Wu 0025
Zhenping Li
Haihong Yang
Zeyuan Wang
Hongbin Ye
Haoran Yu

Directed evolution is a widely-used strategy of protein engineering to improve protein function via mimicking natural mutation and selection. Machine learning-assisted directed evolution (MLDE) approaches aim to learn a fitness predictor, thereby efficiently searching for optimal mutants within the vast combinatorial mutation space. Since annotating mutants is both costly and labor-intensive, how to efficiently sample and utilize informative protein mutants to train the predictor is a critical problem in MLDE. Previous MLDE works just simply utilized pre-trained protein language models (PPLMs) for sampling without tailoring to the specific target protein of interest, which has not fully exploited the potential of PPLMs. In this work, we propose a novel method, the Actively-Finetuned Protein language model for Directed Evolution(AFP-DE), which leverages PPLMs to actively sample and fine-tune themselves, continuously improving the model’s sampling and overall performance through iterations, to achieve efficient directed protein evolution. Extensive experiments have shown the effectiveness of our method in generating optimal mutants with minimal annotation effort, outperforming previous works even with fewer annotated mutants, making it budget-friendly for biological experiments.

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AAAI Conference 2022 Short Paper

Learning to Ask for Data-Efficient Event Argument Extraction (Student Abstract)

Hongbin Ye
Ningyu Zhang
Zhen Bi
Shumin Deng
Chuanqi Tan
Hui Chen
Fei Huang
Huajun Chen

Event argument extraction (EAE) is an important task for information extraction to discover specific argument roles. In this study, we cast EAE as a question-based cloze task and empirically analyze fixed discrete token template performance. As generating human-annotated question templates is often time-consuming and labor-intensive, we further propose a novel approach called “Learning to Ask, ” which can learn optimized question templates for EAE without human annotations. Experiments using the ACE-2005 dataset demonstrate that our method based on optimized questions achieves state-of-the-art performance in both the few-shot and supervised settings.

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AAAI Conference 2021 Conference Paper

Contrastive Triple Extraction with Generative Transformer

Hongbin Ye
Ningyu Zhang
Shumin Deng
Mosha Chen
Chuanqi Tan
Fei Huang
Huajun Chen

Triple extraction is an essential task in information extraction for natural language processing and knowledge graph construction. In this paper, we revisit the end-to-end triple extraction task for sequence generation. Since generative triple extraction may struggle to capture long-term dependencies and generate unfaithful triples, we introduce a novel model, contrastive triple extraction with a generative transformer. Specifically, we introduce a single shared transformer module for encoder-decoder-based generation. To generate faithful results, we propose a novel triplet contrastive training object. Moreover, we introduce two mechanisms to further improve model performance (i. e. , batch-wise dynamic attentionmasking and triple-wise calibration). Experimental results on three datasets (i. e. , NYT, WebNLG, and MIE) show that our approach achieves better performance than that of baselines.

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