Papers by Zikang Wang
Large Language Models in Bioinformatics: A Survey (2025.findings-acl)
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| Challenge: | Large Language Models (LLMs) are revolutionizing bioinformatics, enabling advanced analysis of DNA, RNA, proteins, and single-cell data. |
| Approach: | They examine the evolution of Large Language Models (LLMs) in bioinformatics and precision medicine by focusing on genomic sequence modeling, RNA structure prediction, protein function inference, and single-cell transcriptomics. |
| Outcome: | The proposed models are capable of predicting RNA structure and function and predicting single-cell transcriptomics. |
IDEATE: Detecting AI-Generated Text Using Internal and External Factual Structures (2024.lrec-main)
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| Challenge: | Existing methods to detect AI-generated text rely on internal evidences, but external evidences are not considered. |
| Approach: | They propose a hierarchical graph network that utilizes internal and external factual structures to detect AI-generated text. |
| Outcome: | The proposed network outperforms current state-of-the-art methods on four datasets. |
RBPtool: A Deep Language Model Framework for Multi-Resolution RBP-RNA Binding Prediction and RNA Molecule Design (2025.emnlp-main)
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Jiyue Jiang, Yitao Xu, Zikang Wang, Yihan Ye, Yanruisheng Shao, Yuheng Shan, Jiuming Wang, Xiaodan Fan, Jiao Yuan, Yu Li
| Challenge: | RNA-binding proteins play key roles in post-transcriptional gene regulation . existing methods focus on shallow sequence features or coarse structural representations . large language models allow for precise modeling and biologically informed de novo RNA design . |
| Approach: | They extend RPI15223 into a multi-resolution, structure-level RBP-RNA dataset and introduce RBPtool, a framework that fuses sequence and structural information. |
| Outcome: | The proposed framework achieves state-of-the-art performance on public benchmarks and the RPI15223 dataset while supporting fine-grained level predictions. |
LM2Protein: A Structure-to-Token Protein Large Language Model (2025.findings-emnlp)
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| Challenge: | RNA-binding proteins are critical for various molecular functions, relying on their precise tertiary structures. |
| Approach: | They propose a method to integrate protein 3D structural data within a sequence processing framework. |
| Outcome: | The proposed method achieves high sequence recovery in inverse folding and protein-conditioned RNA design. |
M-RangeDetector: Enhancing Generalization in Machine-Generated Text Detection through Multi-Range Attention Masks (2025.findings-acl)
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| Challenge: | Existing supervised methods for text detection are overfitting within their training domains. |
| Approach: | They propose a method that integrates four distinct attention masking strategies into a Multi-Range Attention module to learn various writing strategies for machine-generated text detection. |
| Outcome: | The proposed method improves the generalization capability of existing detectors on three datasets. |
Knowledge-Enhanced Natural Language Inference Based on Knowledge Graphs (2020.coling-main)
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| Challenge: | Existing approaches to natural language inference rely on semantic knowledge, but background knowledge is limited to a few specific types. |
| Approach: | They propose a Knowledge Graph-enhanced NLI model that leverages background knowledge stored in knowledge graphs to facilitate inference. |
| Outcome: | The proposed model can leverage background knowledge stored in knowledge graphs to perform the task. |
Evaluating the Expressive Appropriateness of Speech in Rich Contexts (2026.acl-long)
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Tianrui Wang, Ziyang Ma, Yizhou Peng, Haoyu Wang, Zhikang Niu, Zikang Huang, Yihao Wu, Yi-Wen Chao, Yu Jiang, Yuheng Lu, Guanrou Yang, Xuanchen Li, Hexin Liu, Chunyu Qiang, Cheng Gong, Yifan Yang, Tianchi Liu, Junyu Wang, Nana Hou, Meng Ge, Fuming You, Yang Wei, Zhongqian Sun, Hu Haifeng, Xiaobao Wang, Eng Siong Chng, Xie Chen, Longbiao Wang, Jianwu Dang
| Challenge: | Existing methods for evaluating expressive speech focus on word accuracy, naturalness, signal quality, or emotional intensity at the utterance level. |
| Approach: | They propose a framework for Evaluating Expressive Appropriateness in speech that assesses whether a speech sample aligns with the underlying communicative intent implied by its discourse-level narrative context. |
| Outcome: | The proposed framework outperforms existing speech evaluation and analysis systems on a human-annotated test set. |
HoWToBench: Holistic Evaluation for LLM’s Capability in Human-level Writing using Tree of Writing (2026.acl-long)
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Andrew Zhuoer Feng, Cunxiang Wang, Yu Luo, Lin Fan, Irene Zhou, Zikang Wang, Xiaotao Gu, Jie Tang, Hongning Wang, Minlie Huang
| Challenge: | Evaluating the writing capabilities of large language models remains a significant challenge due to the multidimensional nature of writing skills and the limitations of existing metrics. |
| Approach: | They propose to model the aggregation weights of sub-features in a tree-structured workflow and propose a Chinese writing benchmark that mitigates biases. |
| Outcome: | The proposed tree-of-writing (ToW) measures the writing capabilities of large language models (LLMs) in Chinese and shows that it mitigates biases and achieves a *0.93* Pearson correlation with human judgments. |
A Survey of Generative Information Extraction (2025.coling-main)
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| Challenge: | Information Extraction (IE) is a popular and fundamental task in natural language processing. |
| Approach: | They first review generative information extraction methods based on pre-trained language models and large language models focusing on their adaptation and generalization capabilities. |
| Outcome: | The proposed methods are based on pre-trained language models and large language models, and emphasize the importance of model collaboration. |